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Add new lineages to emerging_lineages.tsv and color_ordering.tsv #1077

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Jul 31, 2023
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Add new lineages to emerging_lineages.tsv and color_ordering.tsv #1077

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9 changes: 8 additions & 1 deletion defaults/color_ordering.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -34040,8 +34040,15 @@ emerging_lineage BN.1
emerging_lineage CH.1.1
emerging_lineage XAY
emerging_lineage XBC
emerging_lineage FE.1
emerging_lineage XBB.1.9
emerging_lineage XBB.1.9.1
emerging_lineage XBB.1.9.2
emerging_lineage EG.5
emerging_lineage XBB.1.42
emerging_lineage XBB.1.22.1
emerging_lineage XBB.1.19
emerging_lineage XBB.1.17.1
emerging_lineage FE.1
emerging_lineage XBB.2.3

################
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327 changes: 186 additions & 141 deletions defaults/emerging_lineages.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,10 @@ clade gene site alt
20D nuc 13536 T
20D nuc 23731 T

20E (EU1) clade 20A
20E (EU1) nuc 22227 T
20E (EU1) nuc 28932 T
20E (EU1) nuc 29645 T
20E clade 20A
20E nuc 22227 T
20E nuc 28932 T
20E nuc 29645 T

20F clade 20B
20F nuc 1163 T
Expand All @@ -45,143 +45,149 @@ clade gene site alt
20G nuc 28472 T
20G nuc 28869 T

20H (Beta, V2) clade 20C
20H (Beta, V2) nuc 23012 A
20H (Beta, V2) nuc 23063 T
20H (Beta, V2) nuc 23403 G
20H (Beta, V2) nuc 26456 T

20I (Alpha, V1) clade 20B
20I (Alpha, V1) nuc 14676 T
20I (Alpha, V1) nuc 15279 T
20I (Alpha, V1) nuc 23063 T

20J (Gamma, V3) clade 20B
20J (Gamma, V3) nuc 733 C
20J (Gamma, V3) nuc 2749 T
20J (Gamma, V3) nuc 3828 T
20J (Gamma, V3) nuc 5648 C
20J (Gamma, V3) nuc 12778 T
20J (Gamma, V3) nuc 13860 T

21A (Delta) clade 20A
21A (Delta) nuc 21618 G
21A (Delta) nuc 26767 C
21A (Delta) nuc 28461 G

21B (Kappa) clade 20A
21B (Kappa) nuc 17523 T
21B (Kappa) nuc 22917 G
21B (Kappa) nuc 23012 C
21B (Kappa) nuc 27638 C
21B (Kappa) nuc 28881 T
21B (Kappa) nuc 29402 T

21C (Epsilon) clade 20C
21C (Epsilon) nuc 17014 T
21C (Epsilon) nuc 21600 T
21C (Epsilon) nuc 22018 T
21C (Epsilon) nuc 22917 G

21D (Eta) clade 20A
21D (Eta) nuc 14407 T
21D (Eta) nuc 20724 G
21D (Eta) nuc 23593 C
21D (Eta) nuc 24224 C
21D (Eta) nuc 24748 T

21E (Theta) clade 20B
21E (Theta) nuc 12049 T
21E (Theta) nuc 23341 C
21E (Theta) nuc 23604 A
21E (Theta) nuc 24187 A
21E (Theta) nuc 24836 A

21F (Iota) clade 20C
21F (Iota) nuc 16500 C
21F (Iota) nuc 20262 G
21F (Iota) nuc 21575 T
21F (Iota) nuc 22320 G

21G (Lambda) clade 20D
21G (Lambda) nuc 21786 T
21G (Lambda) nuc 21789 T
21G (Lambda) nuc 22917 A
21G (Lambda) nuc 23031 C

21H (Mu) clade 20A
21H (Mu) nuc 3428 G
21H (Mu) nuc 4878 T
21H (Mu) nuc 11451 G
21H (Mu) nuc 13057 T
21H (Mu) nuc 17491 T
21H (Mu) nuc 27925 A

21I (Delta) clade 21A (Delta)
21I (Delta) nuc 5184 T
21I (Delta) nuc 9891 T
21I (Delta) nuc 22227 T

21J (Delta) clade 21A (Delta)
21J (Delta) nuc 11332 G
21J (Delta) nuc 19220 T

21K (Omicron) clade 21M (Omicron)
21K (Omicron) nuc 15240 T
21K (Omicron) nuc 23202 A
21K (Omicron) nuc 23525 T
21K (Omicron) nuc 27259 C

21L (Omicron) clade 21M (Omicron)
21L (Omicron) nuc 21618 T
21L (Omicron) nuc 22775 A

21M (Omicron) clade 20B
21M (Omicron) nuc 18163 G
21M (Omicron) nuc 23599 G

22A (Omicron) clade 21L (Omicron)
22A (Omicron) nuc 12160 A
22A (Omicron) nuc 9866 C
22A (Omicron) nuc 28724 T

22B (Omicron) clade 21L (Omicron)
22B (Omicron) nuc 12160 A
22B (Omicron) nuc 9866 C
22B (Omicron) nuc 27259 A

22C (Omicron) clade 21L (Omicron)
22C (Omicron) nuc 22917 A
22C (Omicron) nuc 23673 T

22D (Omicron) clade 21L (Omicron)
22D (Omicron) nuc 3796 T
22D (Omicron) nuc 26275 G

22E (Omicron) clade 22B (Omicron)
22E (Omicron) nuc 14257 C
22E (Omicron) nuc 16935 A
22E (Omicron) nuc 28312 T
22E (Omicron) nuc 22942 A

22F (Omicron) clade 21L (Omicron)
22F (Omicron) nuc 15461 A
22F (Omicron) nuc 17859 C
22F (Omicron) nuc 23019 C
22F (Omicron) nuc 26275 G

23A (Omicron) clade 22F (Omicron)
23A (Omicron) nuc 22317 T
23A (Omicron) nuc 23018 C
23A (Omicron) nuc 27915 T

BA.2.3.20 clade 21L (Omicron)
20H clade 20C
20H nuc 23012 A
20H nuc 23063 T
20H nuc 23403 G
20H nuc 26456 T

20I clade 20B
20I nuc 14676 T
20I nuc 15279 T
20I nuc 23063 T

20J clade 20B
20J nuc 733 C
20J nuc 2749 T
20J nuc 3828 T
20J nuc 5648 C
20J nuc 12778 T
20J nuc 13860 T

21A clade 20A
21A nuc 21618 G
21A nuc 26767 C
21A nuc 28461 G

21B clade 20A
21B nuc 17523 T
21B nuc 22917 G
21B nuc 23012 C
21B nuc 27638 C
21B nuc 28881 T
21B nuc 29402 T

21C clade 20C
21C nuc 17014 T
21C nuc 21600 T
21C nuc 22018 T
21C nuc 22917 G

21D clade 20A
21D nuc 14407 T
21D nuc 20724 G
21D nuc 23593 C
21D nuc 24224 C
21D nuc 24748 T

21E clade 20B
21E nuc 12049 T
21E nuc 23341 C
21E nuc 23604 A
21E nuc 24187 A
21E nuc 24836 A

21F clade 20C
21F nuc 16500 C
21F nuc 20262 G
21F nuc 21575 T
21F nuc 22320 G

21G clade 20D
21G nuc 21786 T
21G nuc 21789 T
21G nuc 22917 A
21G nuc 23031 C

21H clade 20A
21H nuc 3428 G
21H nuc 4878 T
21H nuc 11451 G
21H nuc 13057 T
21H nuc 17491 T
21H nuc 27925 A

21I clade 21A
21I nuc 5184 T
21I nuc 9891 T
21I nuc 22227 T

21J clade 21A
21J nuc 11332 G
21J nuc 19220 T

21K clade 21M
21K nuc 15240 T
21K nuc 23202 A
21K nuc 23525 T
21K nuc 27259 C

21L clade 21M
21L nuc 21618 T
21L nuc 22775 A

21M clade 20B
21M nuc 18163 G
21M nuc 23599 G

22A clade 21L
22A nuc 12160 A
22A nuc 9866 C
22A nuc 28724 T

22B clade 21L
22B nuc 12160 A
22B nuc 9866 C
22B nuc 27259 A

22C clade 21L
22C nuc 22917 A
22C nuc 23673 T

22D clade 21L
22D nuc 3796 T
22D nuc 26275 G

22E clade 22B
22E nuc 14257 C
22E nuc 16935 A
22E nuc 28312 T
22E nuc 22942 A

22F clade 21L
22F nuc 15461 A
22F nuc 17859 C
22F nuc 23019 C
22F nuc 26275 G

23A clade 22F
23A nuc 22317 T
23A nuc 23018 C
23A nuc 27915 T

23B clade 22F
23B nuc 12730 A
23B nuc 14856 G
23B nuc 18703 T
23B nuc 28447 G

BA.2.3.20 clade 21L
BA.2.3.20 nuc 6770 G
BA.2.3.20 nuc 22332 A
BA.2.3.20 nuc 17678 T
BA.2.3.20 nuc 23013 G

BN.1 clade 22D (Omicron)
BN.1 clade 22D
BN.1 nuc 22599 C
BN.1 nuc 22629 C
BN.1 nuc 23031 C
Expand All @@ -201,25 +207,64 @@ XAY nuc 22899 A
XAY nuc 23679 T
XAY nuc 27575 G

CH.1.1 clade 22D (Omicron)
CH.1.1 clade 22D
CH.1.1 nuc 3857 A
CH.1.1 nuc 23019 C
CH.1.1 nuc 22599 C
CH.1.1 nuc 20741 G
CH.1.1 nuc 22893 C
CH.1.1 nuc 22917 G

FE.1 clade 22F (Omicron)
FE.1 clade 22F
FE.1 nuc 3662 G
FE.1 nuc 8001 G
FE.1 nuc 26012 G

XBB.1.9 clade 22F (Omicron)
XBB.1.9 clade 22F
XBB.1.9 nuc 5720 A
XBB.1.9 nuc 12789 T
XBB.1.9 nuc 28297 C

XBB.2.3 clade 22F (Omicron)
XBB.1.9.1 clade XBB.1.9
XBB.1.9.1 nuc 11956 T
XBB.1.9.1 nuc 23018 C

XBB.1.9.2 clade XBB.1.9
XBB.1.9.2 nuc 16878 T
XBB.1.9.2 nuc 23018 C
XBB.1.9.2 nuc 27507 C

XBB.2.3 clade 22F
XBB.2.3 nuc 4234 T
XBB.2.3 nuc 23123 T
XBB.2.3 nuc 27431 T
XBB.2.3 nuc 27431 T

XBB.1.22.1 clade 22F
XBB.1.22.1 nuc 22161 G
XBB.1.22.1 nuc 23018 C
XBB.1.22.1 nuc 28297 C

XBB.1.42 clade 22F
XBB.1.42 nuc 5720 A
XBB.1.42 nuc 12789 T
XBB.1.42 nuc 16878 T
XBB.1.42 nuc 23401 G
XBB.1.42 nuc 28297 C

XBB.1.17.1 clade 22F
XBB.1.17.1 nuc 1670 T
XBB.1.17.1 nuc 22205 C
XBB.1.17.1 nuc 23018 C
XBB.1.17.1 nuc 27995 C

XBB.1.19 clade 22F
XBB.1.19 nuc 10042 G
XBB.1.19 nuc 21363 T
XBB.1.19 nuc 23018 C
XBB.1.19 nuc 27915 G

EG.5 clade XBB.1.9.2
EG.5 nuc 2334 T
EG.5 nuc 9693 T
EG.5 nuc 22480 T
EG.5 nuc 22930 A
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