From 0ebe5e9cd2bb5efcfad328fe74f63ff5a9a963d3 Mon Sep 17 00:00:00 2001
From: Katherine Eaton <katherine.eaton@phac-aspc.gc.ca>
Date: Tue, 21 Feb 2023 17:13:14 -0600
Subject: [PATCH] script: fix bug in report where it didn't check that plots
 existed

---
 resources/breakpoints_clade.svg | 858 ++++++++++++++++----------------
 resources/issue_to_lineage.tsv  |  36 +-
 resources/issues.tsv            |  64 ++-
 resources/tree.nwk              |   2 +-
 scripts/report.py               |  27 +-
 5 files changed, 514 insertions(+), 473 deletions(-)

diff --git a/resources/breakpoints_clade.svg b/resources/breakpoints_clade.svg
index 80ebec6..a260f8e 100644
--- a/resources/breakpoints_clade.svg
+++ b/resources/breakpoints_clade.svg
@@ -6,7 +6,7 @@
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    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2023-01-24T17:09:50.930323</dc:date>
+    <dc:date>2023-02-21T10:41:43.785659</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
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 L 457.137631 97.465787
 L 351.156321 97.465787
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #3f8fc7"/>
+" clip-path="url(#p53b1a03d27)" style="fill: #3f8fc7"/>
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@@ -51,7 +51,7 @@ L 346.566227 100.319735
 L 346.566227 97.465787
 L 74.804527 97.465787
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #1f77b4"/>
+" clip-path="url(#p53b1a03d27)" style="fill: #1f77b4"/>
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@@ -59,7 +59,7 @@ L 351.143536 100.319735
 L 351.143536 97.465787
 L 346.579013 97.465787
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #d3d3d3"/>
+" clip-path="url(#p53b1a03d27)" style="fill: #d3d3d3"/>
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@@ -67,7 +67,7 @@ L 457.137631 106.02763
 L 457.137631 103.173682
 L 428.177845 103.173682
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #3f8fc7"/>
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@@ -75,7 +75,7 @@ L 417.041433 106.02763
 L 417.041433 103.173682
 L 74.804527 103.173682
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #bfe5ff"/>
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@@ -83,7 +83,7 @@ L 428.165059 106.02763
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 L 417.054218 103.173682
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #d3d3d3"/>
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@@ -91,7 +91,7 @@ L 203.03309 111.735524
 L 203.03309 108.881577
 L 74.804527 108.881577
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #ffc693"/>
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 L 388.094432 108.881577
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@@ -107,7 +107,7 @@ L 269.659776 111.735524
 L 269.659776 108.881577
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 L 208.39033 108.881577
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@@ -139,7 +139,7 @@ L 401.634571 111.735524
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #d3d3d3"/>
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@@ -147,7 +147,7 @@ L 307.032603 117.443419
 L 307.032603 114.589472
 L 74.804527 114.589472
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@@ -155,7 +155,7 @@ L 457.137631 117.443419
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@@ -163,7 +163,7 @@ L 316.148863 117.443419
 L 316.148863 114.589472
 L 307.045389 114.589472
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@@ -171,7 +171,7 @@ L 457.137631 123.151314
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 L 369.030838 120.297366
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@@ -179,7 +179,7 @@ L 367.803404 123.151314
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 L 367.816189 120.297366
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@@ -195,7 +195,7 @@ L 363.481811 128.859209
 L 363.481811 126.005261
 L 128.30022 126.005261
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@@ -203,7 +203,7 @@ L 457.137631 128.859209
 L 457.137631 126.005261
 L 401.915858 126.005261
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@@ -211,7 +211,7 @@ L 110.476847 128.859209
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@@ -219,7 +219,7 @@ L 400.445493 128.859209
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 L 128.287435 126.005261
 L 110.489632 126.005261
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@@ -235,7 +235,7 @@ L 364.69646 128.859209
 L 364.69646 126.005261
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #d3d3d3"/>
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@@ -243,7 +243,7 @@ L 401.903072 128.859209
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@@ -251,7 +251,7 @@ L 143.668725 134.567103
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@@ -259,7 +259,7 @@ L 457.137631 134.567103
 L 457.137631 131.713156
 L 156.659075 131.713156
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@@ -267,7 +267,7 @@ L 156.646289 134.567103
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-" clip-path="url(#p0ae2a3ff2d)" style="fill: #d3d3d3"/>
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@@ -275,7 +275,7 @@ L 146.200309 140.274998
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 L 74.804527 137.421051
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@@ -299,7 +299,7 @@ L 190.554171 145.982893
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 L 272.370361 148.83684
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@@ -347,7 +347,7 @@ L 320.54717 157.398682
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@@ -371,7 +371,7 @@ L 331.223294 163.106577
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diff --git a/resources/issue_to_lineage.tsv b/resources/issue_to_lineage.tsv
index e22b380..a8eeda8 100644
--- a/resources/issue_to_lineage.tsv
+++ b/resources/issue_to_lineage.tsv
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+1622	proposed1622
+1602	proposed1602
 1562	proposed1562
 1553	proposed1553
-1551	proposed1551
 1545	proposed1545
 1538	proposed1538
-1459	XBB.1.5
+1459	XBB.6.1
 1437	proposed1437
-1393	proposed1393
 1367	proposed1367
-1336	proposed1336
 1330	proposed1330
 1273	proposed1273
 1260	proposed1260
@@ -135,4 +154,7 @@
 844	XAY
 844	XBA
 1058	XBB_ARTICv4.1
+1393	proposed1393
+1440	proposed1440
+1576	proposed1576
 844	XAY_dropout
diff --git a/resources/issues.tsv b/resources/issues.tsv
index edf10c3..f61c77b 100644
--- a/resources/issues.tsv
+++ b/resources/issues.tsv
@@ -1,21 +1,29 @@
 issue	lineage	status	status_description	countries	parents_curated	breakpoints_curated	breakpoints	title	date_created	date_updated	date_closed
-1532	XBL	designated			Omicron/CJ.1,Omicron/XBB/22F	5184:15737	Potential breakpoints: 406-3795 (nsp1-nsp3) and 5184-12443 (nsp3-nsp8);The BA.2.75 donor can't be narrowed down at all unless we assume that it provided G3446A. There is no large BA.2.75 branch with G3446A; there are a few small ones that could potentially be the donor but none have been found in Malaysia. One has been found in Kuwait so could be the donor if the recombination happened in the Middle East, but it is BA.2.75.2 so the second breakpoint would have to be between 5184 and 5191 which seems unlikely.	XBB.1/BA.2.75/XBB.1 recombinant with S:F486P (8 seq, Malaysia)	2023-01-07T03:04:13Z	2023-01-10T10:19:45Z	2023-01-09T02:34:29Z
+1637	XBR	designated		 Czech Republic (1/34), Canada-QC (6/34), UK-England (8/34), Israel (2/34), US-CA (17/34)			This is the 6th BA.2.75 x BQ.1 recombinant cluster recently emerged, along with #1393 , #1425 , #1444, #1543 and #1567 . Again this recombinant has a breakpoint at spike.;Potential breakpoint: Spike NTD (22034-22189)	One more BA.2.75 x BQ.1 recombinant with spike breakpoint (39 seqs, 2023-02-19)	2023-02-09T05:42:06Z	2023-02-19T17:13:51Z	2023-02-19T17:13:51Z
+1603	XBB.2.3 XBB.2.4	designated						XBB.2 clusters with S:S486P	2023-01-31T13:07:20Z	2023-02-03T07:05:20Z	NA
+1576	XBT	designated		 Germany (66), Denmark (4), UK (3), Austria (1), Switzerland (1)	Omicron/BA.5/22B,Omicron/BA.2.75/22D,Omicron/BA.5/22B	5184:9865,22600:22628	Recombinant of BA.2.75 -> BA.5.2.34, with the first breakpoint between 5183 and 9766, and the second breakpoint between 22577 and 22898.	BA.5.2.34 -> BA.2.75 -> BA.5.2.34 sandwich recombinant with RBD breakpoint. [142 seqs, Europe]	2023-01-23T21:41:44Z	2023-02-19T17:51:16Z	2023-02-19T17:51:13Z
+1567	XBS	designated		 Malaysia (2/23), Austria (2/23), UK-England (19/23)			This is the 5th BA.2.75 x BQ.1 recombinant cluster recently emerged, along with #1393 , #1425 , #1444 and #1543 . Again this recombinant has a breakpoint at RBD.	Yet another BA.2.75 x BQ.1. recombinant with RBD breakpoint (30 sequences as of 2023-02-12)	2023-01-21T11:52:00Z	2023-02-19T17:22:12Z	2023-02-19T17:22:07Z
+1551	XBK.1	designated						XBK sublineage with S:P1162S mainly in Slovenia and Germany (>180 seq)	2023-01-15T03:24:21Z	2023-02-19T23:56:33Z	2023-02-19T16:33:39Z
+1532	XBL	designated			Omicron/CJ.1,Omicron/XBB/22F	5184:15737	Potential breakpoints: 406-3795 (nsp1-nsp3) and 5184-12443 (nsp3-nsp8);The BA.2.75 donor can't be narrowed down at all unless we assume that it provided G3446A. There is no large BA.2.75 branch with G3446A; there are a few small ones that could potentially be the donor but none have been found in Malaysia. One has been found in Kuwait so could be the donor if the recombination happened in the Middle East, but it is BA.2.75.2 so the second breakpoint would have to be between 5184 and 5191 which seems unlikely.	XBB.1/BA.2.75/XBB.1 recombinant with S:F486P (8 seq, Malaysia)	2023-01-07T03:04:13Z	2023-02-10T17:27:16Z	2023-01-09T02:34:29Z
+1487	XBB.1.13	designated						 XBB.1 sublineage with S:F490P : 68 sequences - Usa , Czechia, Uk, Malaysia, Austria -EDITED as 09/02/23 	2022-12-29T00:39:57Z	2023-02-10T13:16:41Z	2023-02-10T13:16:40Z
 1455	XBB.1.8	designated						XBB.1 with S:186insSGG [14 sequences as of 2022-12-21, Denmark]	2022-12-21T16:47:45Z	2023-01-07T11:19:35Z	2023-01-07T11:19:35Z
-1441	XBM	designated		 US (33 seqs), Canada (17 seqs), India (15 seqs), Denmark (5 seqs), Germany (1 seq), Maritius (1 seq), UK-Scotland (1 seq).	Omicron/BA.2.76,Omicron/BA.5.2	22600:22916	Likely breakpoint: between 22601 and 22915 (Spike S1)	Potential BA.2.76/BF.3 recombinant with spike changes from both donors (110 seqs as of 2023-01-06)	2022-12-17T01:39:48Z	2023-01-10T00:14:56Z	2023-01-09T03:40:33Z
+1441	XBM	designated		 US (33 seqs), Canada (17 seqs), India (15 seqs), Denmark (5 seqs), Germany (1 seq), Maritius (1 seq), UK-Scotland (1 seq).	Omicron/BA.2.76,Omicron/BA.5.2	22600:22916	Likely breakpoint: between 22601 and 22915 (Spike S1)	Potential BA.2.76/BF.3 recombinant with spike changes from both donors (110 seqs as of 2023-01-06)	2022-12-17T01:39:48Z	2023-01-26T16:09:36Z	2023-01-09T03:40:33Z
+1440	XBQ	designated			Omicron/BA.5.2,Omicron/CJ.1	1628:3795		Third CJ.1/BA.5.2 recombinant after XBF and XBK - 68 Sequences defined by Orf1b:M454I	2022-12-16T15:43:54Z	2023-02-19T16:17:58Z	2023-01-17T21:57:51Z
 1428	XBB.1.6	designated		 USA, England, India, Australia				XBB.1 sublineage with S:L216F (38 seqs from USA-CA, England, Australia, India)	2022-12-12T01:27:16Z	2022-12-15T23:47:07Z	2022-12-15T23:46:10Z
 1418	XBK	designated		 Denmark 30, England and Norway 3, the Netherlands, Germany, Japan and USA 2, Sweden and Australia 1.	Omicron/BA.5.2,Omicron/CJ.1	1628:3795		BA.5.2/CJ.1 recombinant, 46 samples from Denmark and 8 other countries	2022-12-08T14:40:19Z	2023-01-06T19:43:50Z	2022-12-15T00:45:03Z
+1393	XBP	designated		 US-TX (3/6), Canada-NB (2/6), France (1/6)	Omicron/BA.2.75/22D,Omicron/BA.5/22B	22191:22330	Potential breakpoint: Spike NTD (22193-22330)	Potential BA.2.75/BQ.1 recombinant (41 seqs as of 2023-01-28)	2022-12-02T06:56:35Z	2023-01-30T18:36:36Z	2023-01-30T18:36:36Z
 1352	XBB.1.4.1	designated		 Denmark (23), Sweden (16), Norway (9), Iceland (1), France (1), Austria (1), Israel (1)				Sublineage of XBB.1.4 with S:S673G (52 seq)	2022-11-18T22:42:38Z	2022-11-25T21:02:42Z	2022-11-25T16:48:04Z
 1296	XBN	designated		 USA (CA, NY, VA, WV)	Omicron/BA.2.75/22D,Omicron/XBB/22F	5184:12443	Potential breakpoint: Between ORF1a:P1640S (present) and ORF1a:N4060S (absent)	BA.2.75 x XBB.3 recombinant [18 as of 2022-11-24, 15x US, 2x CH, 1x India]	2022-11-07T03:33:07Z	2023-01-22T17:21:35Z	2023-01-14T16:30:41Z
 1268	XBJ	designated		 Australia, Austria, Italy, Japan, Singapore, US-TX and US-MN.	Omicron/BA.2/21L,Omicron/BA.5/22B	23019:23039	Potential breakpoint: somewhere between Spike S1 and ORF3a (23015-25809)	Potential BA.2.3.20/BA.5.2 recombinant (25 sequences as of 2022-12-01)	2022-10-31T15:39:30Z	2022-12-06T18:23:27Z	2022-12-01T17:35:03Z
-1259	XBF	designated			Omicron/BA.5/22B,Omicron/BA.2.75/22D	5184:9865	The breakpoint seems to be before 9866. The event seems to have happened very recently, maybe 1-2 months ago as there are no private mutations in the 20k bp downstream of 9866.	BA.5.2.3 x CJ.1 (BM.1.1.1.1) recombinant [AUS-VIC, 9 sequences as of 2022-10-29]	2022-10-29T00:47:58Z	2022-11-11T23:00:16Z	2022-11-03T21:55:05Z
+1259	XBF	designated			Omicron/BA.5/22B,Omicron/BA.2.75/22D	5184:9865	The breakpoint seems to be before 9866. The event seems to have happened very recently, maybe 1-2 months ago as there are no private mutations in the 20k bp downstream of 9866.	BA.5.2.3 x CJ.1 (BM.1.1.1.1) recombinant [AUS-VIC, 9 sequences as of 2022-10-29]	2022-10-29T00:47:58Z	2023-02-14T02:34:45Z	2022-11-03T21:55:05Z
 1246	XBE	designated			Omicron/BA.5.2,Omicron/BA.5.3	22943:27011		Putative recombinant between BA.5.2+Orf1b:1050N+S:346T and BE.4+29868A spotted by @Alurqu and circulating in USA (122 seqs)	2022-10-22T09:58:17Z	2022-10-23T00:59:31Z	2022-10-22T15:14:08Z
 1229	XBH	designated		 Nepal (2/17), Brunei (3/17), UK-England (1/17), France (5/17),  Germany (1/17), Israel (2/17), Malaysia (1/17), Singapore ex-Nepal (1/17), Singapore local (1/17)	Omicron/BA.2.3.17,Omicron/BA.2.75/22D	20236:22000	Potential breakpoint: somewhere between NSP12 and Spike NTD (15451-22000)	Potential BA.2.3.17/BA.2.75.2 recombinant (66 seqs as of 2022-11-12)	2022-10-18T02:24:49Z	2022-11-16T17:34:46Z	2022-11-16T17:34:45Z
 1130	XBC.1	designated						XBC with S:L452M, ORF1a:S391F (6 seq. Philippines, USA, South Korea)	2022-09-28T06:55:38Z	2022-10-05T20:57:05Z	2022-10-03T13:13:39Z
-1100	XBC	designated			Omicron/BA.2/21L,Delta/21I,Omicron/BA.2/21L,Delta/21I	2791:4183,22579:22673,25470:25583		Delta (21I) / BA.2 recombinant (5 seq. Philippines, Austria)	2022-09-22T08:58:44Z	2022-12-15T22:00:36Z	2022-09-24T20:12:47Z
+1100	XBC	designated			Omicron/BA.2/21L,Delta/21I,Omicron/BA.2/21L,Delta/21I	2791:4183,22579:22673,25470:25583		Delta (21I) / BA.2 recombinant (5 seq. Philippines, Austria)	2022-09-22T08:58:44Z	2023-02-10T23:50:11Z	2022-09-24T20:12:47Z
 1088	XBB.1	designated						XBB sublineage with S:G252V  (85 seq. Singapore, Bangladesh, Denmark, UK, Belgium, Australia, Austria as of 03.10.22) 	2022-09-20T08:27:33Z	2022-10-04T12:28:53Z	2022-10-03T13:02:46Z
 911	XAV	designated		 Israel, Sweden, New Zealand, Indonesia, Metropolitan France, France-Reunion, UK (England, Scotland), Canada (ON), US (OH, NJ, NE, MA, CA)	Omicron/BA.2/21L,Omicron/BA.5/22B	12161:22791	Likely breakpoint: 15960-17278 (NSP12/NSP13)	Potential BA.2/BA.5 recombinant (53 sequences as of 2022-08-05)	2022-08-06T02:58:06Z	2022-08-23T13:21:12Z	2022-08-23T13:21:12Z
 896	XBG	designated		 UK (4 in Scotland and 1 in Wales)	Omicron/BA.2.76,Omicron/BA.5.2	22600:22916	Likely breakpoint: between 22601 and 22915 (Spike S1)	Potential BA.2.76/BA.5.2 recombinant with spike changes from both donors (50 seqs as of 2022-11-12)	2022-08-01T08:26:50Z	2022-11-14T17:35:58Z	2022-11-14T17:35:58Z
-895	XAW	designated		 Russia (these 5 sequences are from 5 different patients as per age/sex: M63, F64, M67, F53 and M73)	Delta/21J,Omicron/BA.2/21L,Delta/21J	20056:22577,27875:28310		Potential AY.122/BA.2 recombinant (7 seqs as of 2022-08-19, Russia)	2022-08-01T01:29:42Z	2022-10-19T15:02:42Z	2022-08-25T14:14:08Z
+895	XAW	designated		 Russia (these 5 sequences are from 5 different patients as per age/sex: M63, F64, M67, F53 and M73)	Delta/21J,Omicron/BA.2/21L,Delta/21J	20056:22577,27875:28310		Potential AY.122/BA.2 recombinant (7 seqs as of 2022-08-19, Russia)	2022-08-01T01:29:42Z	2023-02-15T00:10:54Z	2022-08-25T14:14:08Z
 894	XAU	designated			Omicron/BA.1/21K,Omicron/BA.2/21L	2833:4183	Likely breakpoint: 2834-4183 (NSP3)	Potential BA.1.1/BA.2.9 recombinant with likely breakpoint at NSP3 (71 seqs as of 2022-07-30, Spain and other European countries)	2022-07-31T05:11:18Z	2022-08-23T11:10:25Z	2022-08-23T11:10:24Z
 885	XAT	designated		 Japan only	Omicron/BA.2/21L,Omicron/BA.1/21K	26062:26528	Likely breakpoint: between ORF3a and M protein (26062-26528)	Potential recombinant between BA.2.3.13 and BA.1 (67 seqs as of 2022-07-29 in Japan) 	2022-07-29T03:31:23Z	2022-08-22T14:10:27Z	2022-08-22T14:10:27Z
 882	XAS	designated		 USA, Canada, Mexico, Australia, Chile, Colombia, France	Omicron/BA.5/22B,Omicron/BA.2/21L	23041:26528	Likely breakpoint: 27,385-27,787 (based on presence of ORF6:D61L and lack of ORF7b:L11F)	Potential BA.4/BA.5 recombinant with likely breakpoint between ORF6 and ORF7b, or BA.4 lineage missing ORF7b:L11F and N:P151S (65 sequences as of 2022-07-27, mostly USA)	2022-07-27T21:02:47Z	2022-08-22T13:16:37Z	2022-08-22T13:16:36Z
@@ -59,9 +67,12 @@ issue	lineage	status	status_description	countries	parents_curated	breakpoints_cu
 263	XC	designated		 Japan	Delta/21J,Alpha/B.1.1.7/20I	26768:27637		Proposal to redesignate None as recombinant lineage X	2021-10-18T05:19:59Z	2021-11-29T17:13:32Z	2021-11-29T17:12:46Z
 189	XB	designated			B.1.634,B.1.631	22917:23011		Proposal to redesignate B.1.631 as recombinant lineage XB	2021-08-16T18:57:43Z	2021-12-16T02:57:45Z	2021-11-22T11:39:05Z
 63	XA	designated			B.1.177/20E,Alpha/B.1.1.7/20I	21256:21613	Their parental lineages are B.1.1.7 and B.1.177. The breakpoint location was identified as being between base 21255 and base 21764 in reference coordinates.	Proposal to designate a recombinant lineage	2021-04-27T15:53:17Z	2021-05-05T13:43:39Z	2021-05-05T13:42:12Z
-1576	proposed1576	recombinant	recombinant proposal	 Germany (66), Denmark (4), UK (3), Austria (1), Switzerland (1)	Omicron/BA.5/22B,Omicron/BA.2.75/22D,Omicron/BA.5/22B	5184:9865,22600:22628	Recombinant of BA.2.75 -> BA.5.2.34, with the first breakpoint between 5183 and 9766, and the second breakpoint between 22577 and 22898.	BA.5.2.34 -> BA.2.75 -> BA.5.2.34 sandwich recombinant with RBD breakpoint. [75 seqs, Europe]	2023-01-23T21:41:44Z	2023-01-24T08:18:28Z	NA
-1567	proposed1567	recombinant	recombinant proposal	 Malaysia (2/23), Austria (2/23), UK-England (19/23)			This is the 5th BA.2.75 x BQ.1 recombinant cluster recently emerged, along with #1393 , #1425 , #1444 and #1543 . Again this recombinant has a breakpoint at RBD.	Yet another BA.2.75 x BQ.1. recombinant with RBD breakpoint (25 sequences as of 2023-01-24)	2023-01-21T11:52:00Z	2023-01-24T12:52:49Z	NA
-1440	proposed1440	recombinant	recombinant proposal		Omicron/BA.5.2,Omicron/CJ.1	1628:3795		Third CJ.1/BA.5.2 recombinant after XBF and XBK - 68 Sequences defined by Orf1b:M454I	2022-12-16T15:43:54Z	2023-01-17T21:57:51Z	2023-01-17T21:57:51Z
+1674	proposed1674	recombinant	recombinant proposal					Potential BA.2.75/BA.5 recombinant (14 seq., Singapore, USA, UK, Austria)	2023-02-20T13:00:32Z	2023-02-21T10:24:43Z	NA
+1668	proposed1668	recombinant	recombinant proposal	 Chile (all 21)			Breakpoint: Between 22304 and 22893 (S:248 and S:444);Pretty clear breakpoint somewhere in 22304-22893. In addition to ORF1a:M3621V and ORF1a:A4016T, 14/21 sequences have S:A262S. Peculiarly, two of the three nucleotides at S:262 are mutated, including the synonymous mutation T22348A, which has only appeared in 41 other sequences in the last six months.	BF.31.1/BQ.1.10 Recombinant (21 seq, Feb 17)	2023-02-18T00:01:15Z	2023-02-18T10:00:21Z	NA
+1667	proposed1667	recombinant	recombinant proposal				Potential breakpoint:  22034:22189 in RBD	Potential BN.1.2/BQ.1.25 recombinant, similar to XBP but with Spike: R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V (50 sequences in Canada, USA, England...)	2023-02-17T20:46:48Z	2023-02-19T17:56:31Z	2023-02-19T17:56:30Z
+1666	proposed1666	recombinant	recombinant proposal					Possible 5' tip recombinant (BA.5.2) in EF.1.3 (Denmark, ~240 sequences)	2023-02-17T19:18:23Z	2023-02-19T17:55:39Z	NA
+1647	proposed1647	recombinant	recombinant proposal				BA.4.6 is the first 2/3, BA.5.1 the last 1/3, with breakpoints either between S:346-S:658 or after.	Recombinants of BA.4.6 and BA.5.1	2023-02-11T14:33:38Z	2023-02-11T14:33:53Z	NA
+1589	proposed1589	recombinant	recombinant proposal	 Australia (all in NSW)			Potential breakpoint: NSP3, between AA 1307 and 2104	Potential BA.2.75 x XBC.1.1 recombinant (5 sequences as of 2023-01-28)	2023-01-29T11:54:09Z	2023-02-10T16:32:41Z	NA
 1332	proposed1332	recombinant	recombinant proposal	 Canada (37/38 from Ontario and 1/38 from Quebec)			Potential breakpoint: somewhere between E and M proteins (26278-27258)	Potential BA.2.75.2/BF.27 recombinant (40 sequences as of 2022-11-14)	2022-11-14T02:48:27Z	2022-12-26T01:44:14Z	2022-12-26T01:44:14Z
 1305	proposed1305	recombinant	recombinant proposal		Omicron/BA.2.75/22D,Omicron/BA.5.2	27013:27037	It is a recombinant between BA.2.75.2 and BA.5.2.1 (or sublineages of those parents).  The breakpoint is around 27013:27037 bp from the reference strain (Wuhan). Currently it is only circulating in Canada.	BA.2.75.2 and BA.5.2.1 recombinant lineage in Ontario, Canada	2022-11-08T21:54:40Z	2022-11-09T13:36:55Z	NA
 1252	proposed1252	recombinant	recombinant proposal					Multiple different,independent BA.5.2+orf1b:1050N/ BA.5.2.1 recombinants with BQ.1 	2022-10-25T17:18:54Z	2022-11-16T20:56:52Z	2022-11-16T20:56:52Z
@@ -71,16 +82,24 @@ issue	lineage	status	status_description	countries	parents_curated	breakpoints_cu
 781	proposed781	recombinant	recombinant proposal		Omicron/BA.1/21K,Omicron/BA.2/21L	17411:19954	Likely breakpoint: between 17410 and 19995 (NSP13 or NSP14 or NSP15, ORF1b).;We noticed the same breakpoint as in XM #757.	Potential BA.1/BA.2 Recombinant in Brazil, with a likely breakpoint at NSP13-15 (10 Seqs as of 2022-06-22)	2022-06-22T20:56:10Z	2022-08-08T14:10:03Z	2022-08-08T14:08:37Z
 608	proposed608	recombinant	recombinant proposal	 Germany (NW, RP, HH), Israel, Norway, UK (England)	Omicron/BA.2/21L,Omicron/BA.1/21K	24504:26059	- It has interesting double breakpoints and dual ORF3a substitutions;;Likely breakpoint 1: 24506-26048 (Spike S2/ORF3a);Likely breakpoint 2: 27385-29509 (ORF6/N protein), with S2M deletion.	Potential BA.2/BA.1/BA.2 Recombinant with Likely Double Breakpoints (29 Seqs as of 2022-05-06 in Germany, Norway, Israel and UK)	2022-05-07T03:01:50Z	2022-07-21T23:10:00Z	2022-07-21T23:10:00Z
 514	proposed514	recombinant	recombinant proposal	 Uncertain (travellers arrived in Hong Kong from Germany via the Netherlands)	Omicron/BA.1/21K,Omicron/BA.2/21L	20055:21618	Breakpoint: 20055-21618;We detected a recombinant between Omicron subvariants BA.1 and BA.2. It was detected in early Feb from two epidemiologically linked cases. This recombinant has a breakpoint at around the 5' end of spike (20055-21618).;We used Patient 2 sample to clone a RT-PCR product (~2.2k bp) spanning the recombination breakpoint. Both BA.1-specific (19955C/20055A) and BA.2-specific (21618T/21633-21641del) SNPs can be detected in the same plasmid clone, confirming that Patients 1 and 2 were indeed infected by a BA.1/BA.2 recombinant virus.	BA.2/BA.1 Recombinant with breakpoint at 20055-21618 detected in travellers arriving in Hong Kong, February 2022	2022-04-02T12:14:42Z	2022-10-12T07:43:47Z	2022-10-12T07:43:47Z
+1669	proposed1669	monitor	currently too small, watch for future developments	 all sequences are from Australia, but from 4 different states, including NSW (6/11), VIC (2/11), SA (2/11) and QLD (1/11).			Potential breakpoint: NSP16 or Spike RBD (21055-22916)	BR.2.1 x XBF recombinant (11 sequences as of 2023-02-17, from 4 states of Australia)	2023-02-18T04:21:25Z	2023-02-19T17:59:09Z	NA
+1653	proposed1653	monitor	currently too small, watch for future developments					Possible recombinant lineage between BR.2.1 and CJ.1 (or XBF or XBK)   defined by ORF1b:R2613H ,S:I486P S:L452L(rev), S:F490S  ,Orf8:S82T, Orf8:S67S (rev) - 11 sequences 	2023-02-13T15:15:49Z	2023-02-18T09:16:11Z	2023-02-18T09:15:47Z
+1644	proposed1644	monitor	currently too small, watch for future developments					Potential XBB.1.5/BA.5 recombinant (5 seq., Canada)	2023-02-10T07:42:27Z	2023-02-10T15:17:55Z	NA
+1642	proposed1642	monitor	currently too small, watch for future developments				Breakpoint somewhere in ORF1b (>17k) or Spike (<23k).	Potentially first mainland China recombinant: BA.5.2.48 x BF.7.14 [2 seq, Anhui]	2023-02-09T22:31:01Z	2023-02-19T09:47:33Z	NA
+1641	proposed1641	monitor	currently too small, watch for future developments	 Denmark, 5			Breakpoint: between nucleotide 9866 and 12160	Description: BA.5.11 sublineage(#1640)/XBK recombinant, 6 samples from Denmark	2023-02-09T17:25:31Z	2023-02-21T13:33:54Z	NA
+1614	XBB.1.5.10	monitor	currently too small, watch for future developments					XBB.1.5 with S:F456L and Orf1b:A1643V apparently growing fastly in North Carolina , USA (48 sequences)	2023-02-03T13:15:44Z	2023-02-10T15:13:44Z	2023-02-10T13:05:22Z
 1543	proposed1543	monitor	currently too small, watch for future developments	 Singapore ex-Vietnam (1/5), Singapore local case (2/5), Germany (1/5), US-CA (1/5)				Another BA.2.75/BQ.1 recombinant with RBD breakpoint (6 sequences as of 2022-01-13)	2023-01-11T00:59:34Z	2023-01-13T13:45:35Z	NA
-1505	proposed1505	monitor	currently too small, watch for future developments	 US-NY			Potential breakpoint: ORF3a/E (25417-26274)	Potential XBB.1.5/BQ.1.14 recombinant (3 sequences as of 2023-01-19)	2023-01-01T03:16:29Z	2023-01-20T09:58:26Z	NA
-1460	proposed1460	monitor	currently too small, watch for future developments				I've come across a BA.5 - XBB.1 recombinant with BA.5 5' end and breakpoint before Spike, around nt pos 20000.	CR.1 (BA.5.2.18.1) x XBB.1 recombinant [5 seq, 2x UK, 1x US, 1x FR, 1x DK]	2022-12-22T16:43:04Z	2023-01-24T08:12:54Z	NA
-1444	proposed1444	monitor	currently too small, watch for future developments	 Korea (1/8), France (1/8), Germany (1/8), US-KS (1/8), New Caledocia (1/8), Italy (3/8)	Omicron/BA.2.75/22D,Omicron/BA.5/22B	22600:22628	Potential breakpoint: Spike NTD (22580-22939)	Another BA.2.75/BQ.1 recombinant similar to #1393 and #1425 (21 seqs as of 2023-01-20)	2022-12-19T04:43:24Z	2023-01-22T11:54:21Z	NA
-1425	proposed1425	monitor	currently too small, watch for future developments	 Japan-Fukushima (3/6),  Malaysia-Selangor (2/6), Australia-Sydney (1/6),	Omicron/CJ.1,Omicron/BA.5.3,Omicron/CJ.1	22578:22892,25417:26274	Potential breakpoint: Spike NTD (22577, 22893) and (25416, 26275)	BA.2.75 x BQ.1 x BA.2.75 recombinant [19 seqs, Malaysia, Japan, Thailand, Singapore, Australia, Netherlands, Singapore]	2022-12-10T21:24:00Z	2023-01-21T15:12:40Z	NA
-1362	proposed1362	monitor	currently too small, watch for future developments					Potential BA.2/BA.5 recombinant (6 seqs., UK) 	2022-11-23T11:05:05Z	2022-11-25T13:10:57Z	NA
+1535	XBB.2.3	monitor	currently too small, watch for future developments					XBB.2  with S:F486P,S:P521S - 11 sequences USA, India as 25-01-23	2023-01-08T08:52:54Z	2023-01-31T14:38:05Z	2023-01-31T13:30:45Z
+1505	proposed1505	monitor	currently too small, watch for future developments	 US-NY			Potential breakpoint: ORF3a/E (25417-26274)	Potential XBB.1.5/BQ.1.14 recombinant (8 sequences as of 2023-02-17)	2023-01-01T03:16:29Z	2023-02-18T04:29:53Z	NA
+1490	XBB.1.11 XBB.1.11.1	monitor	currently too small, watch for future developments					Another XBB.1 sublineage with S:F486P (12 seq, mainly SE Asia)	2022-12-29T17:58:22Z	2023-01-31T14:37:03Z	2023-01-31T14:36:52Z
+1460	proposed1460	monitor	currently too small, watch for future developments				I've come across a BA.5 - XBB.1 recombinant with BA.5 5' end and breakpoint before Spike, around nt pos 20000.	CR.1 (BA.5.2.18.1) x XBB.1 recombinant [5 seq, 2x UK, 1x US, 1x FR, 1x DK]	2022-12-22T16:43:04Z	2023-02-13T09:39:10Z	NA
+1444	proposed1444	monitor	currently too small, watch for future developments	 Korea (1/8), France (1/8), Germany (1/8), US-KS (1/8), New Caledocia (1/8), Italy (3/8)	Omicron/BA.2.75/22D,Omicron/BA.5/22B	22600:22628	Potential breakpoint: Spike NTD (22580-22939)	Another BA.2.75/BQ.1 recombinant similar to #1393 and #1425 (26 seqs as of 2023-02-10)	2022-12-19T04:43:24Z	2023-02-10T16:37:13Z	NA
+1425	proposed1425	monitor	currently too small, watch for future developments	 Japan-Fukushima (3/6),  Malaysia-Selangor (2/6), Australia-Sydney (1/6),	Omicron/CJ.1,Omicron/BA.5.3,Omicron/CJ.1	22578:22892,25417:26274	Potential breakpoint: Spike NTD (22577, 22893) and (25416, 26275)	BA.2.75 x BQ.1 x BA.2.75 recombinant [27 seqs, many countries, continents]	2022-12-10T21:24:00Z	2023-02-20T15:26:53Z	NA
+1362	proposed1362	monitor	currently too small, watch for future developments					Potential BA.2/BA.5 recombinant (6 seqs., UK) 	2022-11-23T11:05:05Z	2023-02-06T15:40:27Z	2023-02-06T15:40:27Z
 1360	proposed1360	monitor	currently too small, watch for future developments	 France				BA.2.75/BA.5 Recombinant with S:K986Q & other private mutations (France, 8 seq)	2022-11-22T20:51:49Z	2022-12-17T15:58:40Z	2022-12-17T15:58:40Z
 1340	proposed1340	monitor	currently too small, watch for future developments	 Singapore	Omicron/BA.2.75/22D,Omicron/XBB/22F	20236:21809	Potential breakpoint: somewhere between ORF1b and Spike NTD (16345 to 21808).	Potential BN.1.3/XBB.1 recombinant with multiple private mutations in N protein (2 sequences as of 2022-11-14)	2022-11-15T08:42:38Z	2022-12-26T01:44:56Z	2022-12-26T01:44:55Z
 1255	XAY.1.1	monitor	currently too small, watch for future developments					XAY.1 with S:346T (1 sequence, South Africa)	2022-10-26T18:56:28Z	2022-11-02T23:44:50Z	2022-11-02T23:44:50Z
-1218	proposed1218	monitor	currently too small, watch for future developments				I cam across a few sequences that had a Spike very similar to XBB - but with breakpoint a little bit different, as it contains the BA.2.75 S:257S	Potential recombinant, similar to XBB, maybe similar parents or even involving it	2022-10-15T18:36:41Z	2022-10-15T18:36:51Z	NA
+1218	proposed1218	monitor	currently too small, watch for future developments				I cam across a few sequences that had a Spike very similar to XBB - but with breakpoint a little bit different, as it contains the BA.2.75 S:257S	Potential recombinant, similar to XBB, maybe similar parents or even involving it	2022-10-15T18:36:41Z	2023-02-19T17:52:22Z	2023-02-19T17:52:22Z
 1208	XAY.1	monitor	currently too small, watch for future developments					XAY sublineage with S:D253G (6 seq., South Africa, USA)	2022-10-12T07:10:20Z	2022-10-15T23:49:25Z	2022-10-15T23:49:25Z
 1185	proposed1185	monitor	currently too small, watch for future developments				Looks to be a recombinant between BA.2/BA.5, breakpoint between Spike 70 and 452 with the addition of S:T547K and S:S1147L	Potential BA.2/BA.5 recombinant lineage with S:T547K and S:S1147L (13 Examples, mainly Belgium)	2022-10-07T14:58:07Z	2022-12-05T11:02:10Z	2022-12-05T11:02:10Z
 1175	XBB.4	monitor	currently too small, watch for future developments					XBB with S:444R [2 seqs, India]	2022-10-06T17:53:17Z	2022-10-20T19:08:30Z	2022-10-20T19:08:19Z
@@ -103,16 +122,16 @@ issue	lineage	status	status_description	countries	parents_curated	breakpoints_cu
 439	proposed439	not accepted	A proposal for a new lineage has not been accepted		Delta/21J,Omicron/BA.1/21K	21988:22577	Breakpoint: between Spike NTD/RBD nuc 22199-22576	Potential US East Coast BA.1.1/AY.119 recombinant (7 seq) [potentially the one monitored by UKHSA]	2022-02-14T19:09:24Z	2022-05-11T14:33:17Z	2022-05-11T14:33:09Z
 422	proposed422	not accepted	A proposal for a new lineage has not been accepted					Possible English recombinant descended from Omicron and Delta (UKHSA signal under monitoring)	2022-01-31T07:44:42Z	2022-05-11T15:09:41Z	2022-05-11T15:09:34Z
 210	proposed210	not accepted	A proposal for a new lineage has not been accepted	 Korea (12 sequences); Korea (9 sequences); Spain (3 sequences), Belgium (1), Germany (1), France (1), Korea ex-UAE (1)				3 small clades with interesting (recombinant-look-alike) mutations	2021-09-06T02:04:47Z	2021-10-12T17:14:00Z	2021-10-12T17:14:00Z
-1562	proposed1562	recombinant sublineage						XBC.2 with S:F486L circulating in Brunei (28 sequences )	2023-01-18T20:34:33Z	2023-01-18T21:35:45Z	NA
-1553	proposed1553	recombinant sublineage						XAY.1 sublineage with ORF1a:V86I (18 seq. Slovenia, Germany)	2023-01-15T03:49:42Z	2023-01-16T08:07:47Z	NA
-1551	proposed1551	recombinant sublineage						XBK sublineage with S:P1162S mainly in Slovenia and Germany (>40 seq)	2023-01-15T03:24:21Z	2023-01-16T08:07:14Z	NA
+1651	proposed1651	recombinant sublineage		 Australia (15), Singapore (2)				XBF Sublineage with S:P621S (24 seq, Feb 20)	2023-02-13T11:31:18Z	2023-02-21T01:41:41Z	NA
+1622	proposed1622	recombinant sublineage						XBC.1 with S:G184S, ORF1a:P3952S, ORF1a:V4072A  (42 seq., Australia, Singapore)	2023-02-06T08:41:51Z	2023-02-20T14:24:20Z	2023-02-20T14:24:20Z
+1602	proposed1602	recombinant sublineage						RFC: XBB.1.9 with S:S486P	2023-01-31T11:57:44Z	2023-02-10T01:14:10Z	2023-02-03T06:48:08Z
+1562	proposed1562	recombinant sublineage						XBC.2 with S:F486L circulating in Brunei (28 sequences )	2023-01-18T20:34:33Z	2023-01-30T14:25:04Z	2023-01-30T14:25:04Z
+1553	proposed1553	recombinant sublineage						XAY.1 sublineage with ORF1a:V86I (46 seq. Slovenia, Germany, Croatia, US)	2023-01-15T03:49:42Z	2023-02-16T21:36:03Z	NA
 1545	proposed1545	correction	Highlight an error in the description or definition					Correction - Recombinants with duplicate references on alias_key.json	2023-01-11T20:10:07Z	2023-01-12T04:24:22Z	2023-01-12T04:24:22Z
-1538	proposed1538	recombinant sublineage		 Australia - Western, Victoria, Tasmania				XBC.2 sublineage with S:K444T [13 seqs, Australia]	2023-01-09T22:24:50Z	2023-01-24T17:38:39Z	NA
-1459	XBB.1.5	XBB	proposed sublineage of XBB					XBB with S:486P from US east coast  - artefact or homoplasy? [9 sequences US, 1 AUS]	2022-12-22T15:44:32Z	2023-01-09T17:50:29Z	2023-01-09T04:19:08Z
+1538	proposed1538	recombinant sublineage		 Australia - Western, Victoria, Tasmania				XBC.2 sublineage with S:K444T [17 seqs, Australia]	2023-01-09T22:24:50Z	2023-02-14T14:49:59Z	NA
+1459	XBB.6.1	XBB	proposed sublineage of XBB					XBB with S:486P from US east coast  - artefact or homoplasy? [9 sequences US, 1 AUS]	2022-12-22T15:44:32Z	2023-01-31T13:34:11Z	2023-01-09T04:19:08Z
 1437	proposed1437						since WHO declared XBB as variant under monitoring (VUM), I tried to find the breakpoint and the p-value.;could find a breakpoint at position 28370 and 29836 with a siginificant p-value.	validation of recombinant lineages	2022-12-15T11:59:54Z	2022-12-20T22:53:57Z	2022-12-15T17:47:01Z
-1393	proposed1393	recommended	Recommended for designation by pango team member	 US-TX (3/6), Canada-NB (2/6), France (1/6)	Omicron/BA.2.75/22D,Omicron/BA.5/22B	22191:22330	Potential breakpoint: Spike NTD (22193-22330)	Potential BA.2.75/BQ.1 recombinant (37 seqs as of 2023-01-20)	2022-12-02T06:56:35Z	2023-01-22T12:29:20Z	NA
 1367	proposed1367	recombinant sublineage						XBC.1 sublineage with S:G476S circulating in Australia (8 sequences - 4 states NSW, VIC, QLD, TAS)	2022-11-25T15:29:55Z	2022-12-04T21:42:18Z	2022-12-04T21:42:18Z
-1336	proposed1336	recombinant sublineage						XBB with S:G257S (12 seq. India, Singapore, USA, Austria)	2022-11-14T16:10:08Z	2022-11-14T18:22:11Z	NA
 1330	proposed1330	recombinant sublineage		 About 19 countries				Sublineage(s) of XBB with S:H146K (~135 seq, ~19 countries)	2022-11-13T14:04:56Z	2022-12-19T06:35:15Z	2022-12-17T15:33:04Z
 1273	proposed1273							Should recombinant alias keys all use unaliased names for parity	2022-11-01T16:06:33Z	2022-11-02T13:16:47Z	2022-11-01T16:20:52Z
 1260	proposed1260	recombinant sublineage						XBD sublineage with S:N188S circulating in Hong Kong 24 sequences 	2022-10-29T19:11:28Z	2022-12-18T14:04:51Z	2022-12-18T14:04:51Z
@@ -136,4 +155,7 @@ issue	lineage	status	status_description	countries	parents_curated	breakpoints_cu
 844	XAY				Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L	6403:8985,9867:10197,12881:15450,21847:22199,24470:24999,27385:27637					
 844	XBA				Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L,Delta/21J	2791:4180,21847:22199,24470:24999					
 1058	XBB_ARTICv4.1				Omicron/BA.2.10,Omicron/BA.2.75/22D	22191:22576					
+1393	proposed1393				Omicron/BA.2.75/22D,Omicron/BA.5/22B	22191:22330					
+1440	proposed1440				Omicron/BA.5.2,Omicron/CJ.1	1628:3795					
+1576	proposed1576				Omicron/BA.5/22B,Omicron/BA.2.75/22D,Omicron/BA.5/22B	5184:9865,22600:22628					
 844	XAY_dropout				Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L,Delta/21J,Omicron/BA.2/21L	6403:8985,9867:10197,12881:15450,20056:22199,24470:24999,27385:27637					
diff --git a/resources/tree.nwk b/resources/tree.nwk
index 449912b..de87059 100644
--- a/resources/tree.nwk
+++ b/resources/tree.nwk
@@ -1 +1 @@
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8:1.00000,B.1.520:1.00000,B.1.521:1.00000,B.1.523:1.00000,B.1.524:1.00000,B.1.525:1.00000,B.1.526:1.00000,B.1.527:1.00000,B.1.528:1.00000,B.1.529:1.00000,B.1.530:1.00000,B.1.531:1.00000,B.1.532:1.00000,B.1.533:1.00000,B.1.534:1.00000,B.1.535:1.00000,B.1.536:1.00000,B.1.537:1.00000,B.1.538:1.00000,B.1.539:1.00000,B.1.540:1.00000,B.1.541:1.00000,B.1.542:1.00000,B.1.543:1.00000,B.1.544:1.00000,B.1.545:1.00000,B.1.546:1.00000,B.1.547:1.00000,B.1.548:1.00000,B.1.549:1.00000,B.1.550:1.00000,B.1.551:1.00000,B.1.552:1.00000,B.1.554:1.00000,B.1.555:1.00000,B.1.556:1.00000,B.1.557:1.00000,B.1.558:1.00000,B.1.559:1.00000,B.1.560:1.00000,B.1.561:1.00000,B.1.562:1.00000,B.1.563:1.00000,(B.1.564.1:1.00000)B.1.564:1.00000,B.1.565:1.00000,B.1.566:1.00000,B.1.567:1.00000,B.1.568:1.00000,B.1.569:1.00000,B.1.570:1.00000,B.1.571:1.00000,B.1.572:1.00000,B.1.573:1.00000,B.1.574:1.00000,(B.1.575.1:1.00000,B.1.575.2:1.00000)B.1.575:1.00000,B.1.576:1.00000,B.1.577:1.00000,B.1.578:1.00000,B.1.579:1.00000,B.1.580:1.00000,B.1.581:1.00000,B.1.582:1.00000,B.1.585:1.00000,B.1.586:1.00000,B.1.587:1.00000,(B.1.588.1:1.00000)B.1.588:1.00000,B.1.589:1.00000,B.1.590:1.00000,B.1.591:1.00000,B.1.592:1.00000,B.1.593:1.00000,B.1.594:1.00000,(B.1.595.1:1.00000,B.1.595.2:1.00000,B.1.595.3:1.00000,B.1.595.4:1.00000)B.1.595:1.00000,(B.1.596.1:1.00000)B.1.596:1.00000,B.1.597:1.00000,B.1.598:1.00000,B.1.599:1.00000,B.1.600:1.00000,B.1.601:1.00000,B.1.602:1.00000,B.1.603:1.00000,B.1.604:1.00000,B.1.605:1.00000,B.1.606:1.00000,B.1.607:1.00000,B.1.609:1.00000,B.1.610:1.00000,B.1.611:1.00000,B.1.612:1.00000,B.1.613:1.00000,B.1.614:1.00000,B.1.615:1.00000,B.1.616:1.00000,(B.1.617.1:1.00000,(AY.1:1.00000,AY.2:1.00000,(AY.3.1:1.00000,AY.3.2:1.00000,AY.3.3:1.00000,AY.3.4:1.00000)AY.3:1.00000,(AY.4.1:1.00000,(AY.4.2.1:1.00000,AY.4.2.2:1.00000,AY.4.2.3:1.00000,AY.4.2.4:1.00000,AY.4.2.5:1.00000)AY.4.2:1.00000,AY.4.3:1.00000,AY.4.4:1.00000,AY.4.5:1.00000,AY.4.6:1.00000,AY.4.7:1.00000,AY.4.8:1.00000,AY.4.9:1.00000,AY.4.10:1.00000,AY.4.11:1.00000,AY.4.12:1.00000,AY.4.13:1.00000,AY.4.14:1.00000,AY.4.15:1.00000,AY.4.16:1.00000,AY.4.17:1.00000)AY.4:1.00000,(AY.5.1:1.00000,AY.5.2:1.00000,AY.5.3:1.00000,AY.5.4:1.00000,AY.5.5:1.00000,AY.5.6:1.00000,AY.5.7:1.00000)AY.5:1.00000,AY.6:1.00000,(AY.7.1:1.00000,AY.7.2:1.00000)AY.7:1.00000,AY.8:1.00000,((AY.9.2.1:1.00000,AY.9.2.2:1.00000)AY.9.2:1.00000)AY.9:1.00000,AY.10:1.00000,AY.11:1.00000,AY.13:1.00000,AY.14:1.00000,AY.15:1.00000,(AY.16.1:1.00000)AY.16:1.00000,AY.17:1.00000,AY.18:1.00000,AY.19:1.00000,(AY.20.1:1.00000)AY.20:1.00000,AY.21:1.00000,AY.22:1.00000,(AY.23.1:1.00000,AY.23.2:1.00000)AY.23:1.00000,(AY.24.1:1.00000)AY.24:1.00000,((AY.25.1.1:1.00000,AY.25.1.2:1.00000)AY.25.1:1.00000,AY.25.2:1.00000,AY.25.3:1.00000)AY.25:1.00000,(AY.26.1:1.00000)AY.26:1.00000,AY.27:1.00000,AY.28:1.00000,(AY.29.1:1.00000,AY.29.2:1.00000)AY.29:1.00000,AY.30:1.00000,AY.31:1.00000,AY.32:1.00000,(AY.33.1:1.00000,AY.33.2:1.00000)AY.33:1.00000,((AY.34.1.1:1.00000)AY.34.1:1.00000,AY.34.2:1.00000)AY.34:1.00000,AY.35:1.00000,(AY.36.1:1.00000)AY.36:1.00000,AY.37:1.00000,AY.38:1.00000,((AY.39.1.1:1.00000,AY.39.1.2:1.00000,AY.39.1.3:1.00000,AY.39.1.4:1.00000)AY.39.1:1.00000,AY.39.2:1.00000,AY.39.3:1.00000)AY.39:1.00000,AY.40:1.00000,AY.41:1.00000,(AY.42.1:1.00000)AY.42:1.00000,(AY.43.1:1.00000,AY.43.2:1.00000,AY.43.3:1.00000,AY.43.4:1.00000,AY.43.5:1.00000,AY.43.6:1.00000,AY.43.7:1.00000,AY.43.8:1.00000,AY.43.9:1.00000)AY.43:1.00000,AY.44:1.00000,AY.45:1.00000,(AY.46.1:1.00000,AY.46.2:1.00000,AY.46.3:1.00000,AY.46.4:1.00000,AY.46.5:1.00000,(AY.46.6.1:1.00000)AY.46.6:1.00000)AY.46:1.00000,AY.47:1.00000,AY.48:1.00000,AY.49:1.00000,AY.50:1.00000,AY.51:1.00000,AY.52:1.00000,AY.53:1.00000,AY.54:1.00000,AY.55:1.00000,AY.56:1.00000,AY.57:1.00000,AY.58:1.00000,AY.59:1.00000,AY.60:1.00000,AY.61:1.00000,AY.62:1.00000,AY.63:1.00000,AY.64:1.00000,AY.65:1.00000,AY.66:1.00000,AY.67:1.00000,AY.68:1.00000,AY.69:1.00000,AY.70:1.00000,AY.71:1.00000,AY.72:1.00000,AY.73:1.00000,AY.74:1.00000,(AY.75.2:1.00000,AY.75.3:1.00000)AY.75:1.00000,AY.76:1.00000,AY.77:1.00000,AY.78:1.00000,AY.79:1.00000,AY.80:1.00000,AY.81:1.00000,AY.82:1.00000,AY.83:1.00000,AY.84:1.00000,AY.85:1.00000,AY.86:1.00000,AY.87:1.00000,AY.88:1.00000,AY.90:1.00000,(AY.91.1:1.00000)AY.91:1.00000,AY.92:1.00000,AY.93:1.00000,AY.94:1.00000,AY.95:1.00000,((AY.98.1.1:1.00000)AY.98.1:1.00000)AY.98:1.00000,(AY.99.1:1.00000,AY.99.2:1.00000)AY.99:1.00000,AY.100:1.00000,AY.101:1.00000,(AY.102.1:1.00000,AY.102.2:1.00000)AY.102:1.00000,(AY.103.1:1.00000,AY.103.2:1.00000)AY.103:1.00000,AY.104:1.00000,AY.105:1.00000,AY.106:1.00000,AY.107:1.00000,AY.108:1.00000,AY.109:1.00000,AY.110:1.00000,AY.111:1.00000,(AY.112.1:1.00000,AY.112.2:1.00000,AY.112.3:1.00000)AY.112:1.00000,AY.113:1.00000,AY.114:1.00000,(AY.116.1:1.00000)AY.116:1.00000,AY.117:1.00000,AY.118:1.00000,(AY.119.1:1.00000,AY.119.2:1.00000)AY.119:1.00000,(AY.120.1:1.00000,(AY.120.2.1:1.00000)AY.120.2:1.00000)AY.120:1.00000,(AY.121.1:1.00000)AY.121:1.00000,(AY.122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diff --git a/scripts/report.py b/scripts/report.py
index f910ebc..af676ff 100755
--- a/scripts/report.py
+++ b/scripts/report.py
@@ -70,9 +70,7 @@ def main(
     plot_suffix = ".png"
     df_suffix = ".tsv"
     labels = [
-        f.replace(plot_suffix, "")
-        for f in os.listdir(plot_dir)
-        if f.endswith(plot_suffix)
+        f.replace(df_suffix, "") for f in os.listdir(plot_dir) if f.endswith(df_suffix)
     ]
 
     plot_dict = {}
@@ -114,7 +112,6 @@ def main(
     # General Summary
 
     # Slide setup
-    plot_path = plot_dict["lineage"]["plot_path"]
     graph_slide_layout = presentation.slide_layouts[8]
     slide = presentation.slides.add_slide(graph_slide_layout)
     title = slide.shapes.title
@@ -123,6 +120,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["lineage"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]
@@ -207,8 +205,6 @@ def main(
         if status not in plot_dict:
             continue
 
-        plot_path = plot_dict[status]["plot_path"]
-
         # Slide setup
         graph_slide_layout = presentation.slide_layouts[8]
         slide = presentation.slides.add_slide(graph_slide_layout)
@@ -219,8 +215,10 @@ def main(
 
         chart_placeholder = slide.placeholders[1]
         # Plotting may have failed to create an individual figure
+        plot_path = plot_dict[status]["plot_path"]
         if os.path.exists(plot_path):
             chart_placeholder.insert_picture(plot_path)
+
         body = slide.placeholders[2]
 
         # Stats
@@ -257,7 +255,6 @@ def main(
     # ---------------------------------------------------------------------
     # Geographic Summary
 
-    plot_path = plot_dict["geography"]["plot_path"]
     geo_df = plot_dict["geography"]["df"]
     geos = list(geo_df.columns)
     geos.remove("epiweek")
@@ -276,8 +273,10 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["geography"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
+
     body = slide.placeholders[2]
 
     summary = "\n"
@@ -303,7 +302,6 @@ def main(
     # ---------------------------------------------------------------------
     # Largest Summary
 
-    plot_path = plot_dict["largest"]["plot_path"]
     largest_df = plot_dict["largest"]["df"]
 
     largest_geos = list(largest_df.columns)
@@ -336,6 +334,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["largest"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]
@@ -368,7 +367,6 @@ def main(
     # ---------------------------------------------------------------------
     # RBD Levels
 
-    plot_path = plot_dict["rbd_level"]["plot_path"]
     rbd_df = plot_dict["rbd_level"]["df"]
     rbd_levels = list(rbd_df.columns)
     rbd_levels.remove("epiweek")
@@ -391,6 +389,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["rbd_level"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]
@@ -417,7 +416,6 @@ def main(
     # ---------------------------------------------------------------------
     # Parents Summary (Clade)
 
-    plot_path = plot_dict["parents_clade"]["plot_path"]
     parents_df = plot_dict["parents_clade"]["df"]
 
     parents = list(parents_df.columns)
@@ -437,6 +435,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["parents_clade"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]
@@ -463,7 +462,6 @@ def main(
     # ---------------------------------------------------------------------
     # Parents Summary (Lineage)
 
-    plot_path = plot_dict["parents_lineage"]["plot_path"]
     parents_df = plot_dict["parents_lineage"]["df"]
 
     parents = list(parents_df.columns)
@@ -483,6 +481,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["parents_lineage"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]
@@ -509,8 +508,6 @@ def main(
     # ---------------------------------------------------------------------
     # Breakpoints Clade Summary
 
-    plot_path = plot_dict["breakpoints_clade"]["plot_path"]
-
     graph_slide_layout = presentation.slide_layouts[8]
     slide = presentation.slides.add_slide(graph_slide_layout)
     title = slide.shapes.title
@@ -520,6 +517,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["breakpoints_clade"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]
@@ -527,8 +525,6 @@ def main(
     # ---------------------------------------------------------------------
     # Breakpoints Lineage Summary
 
-    plot_path = plot_dict["breakpoints_lineage"]["plot_path"]
-
     graph_slide_layout = presentation.slide_layouts[8]
     slide = presentation.slides.add_slide(graph_slide_layout)
     title = slide.shapes.title
@@ -538,6 +534,7 @@ def main(
 
     chart_placeholder = slide.placeholders[1]
     # Plotting may have failed to create an individual figure
+    plot_path = plot_dict["breakpoints_lineage"]["plot_path"]
     if os.path.exists(plot_path):
         chart_placeholder.insert_picture(plot_path)
     body = slide.placeholders[2]