Run ID: SRR2101471
Sample name:
Date: 03-04-2023 23:44:18
Number of reads: 601544
Percentage reads mapped: 93.71
Strain: lineage4.4.1.1
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.4 | Euro-American | S;T | None | 1.0 |
lineage4.4.1 | Euro-American (S-type) | S;T | None | 1.0 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761127 | p.Ser441Ala | missense_variant | 0.11 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6905 | p.Ile556Val | missense_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9138 | p.Gln613Glu | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
ccsA | 620748 | c.858T>G | synonymous_variant | 0.25 |
ccsA | 620859 | c.969G>T | synonymous_variant | 0.1 |
rpoB | 761088 | c.1282_1284delAGCinsTCG | synonymous_variant | 0.13 |
rpoB | 761097 | c.1291_1292delAGinsTC | synonymous_variant | 0.14 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.15 |
rpoB | 761132 | c.1326G>C | synonymous_variant | 0.11 |
rpoB | 761133 | c.1327T>C | synonymous_variant | 0.11 |
rpoB | 761138 | c.1332C>G | synonymous_variant | 0.1 |
rpoB | 761147 | c.1341C>T | synonymous_variant | 0.11 |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.11 |
rpoB | 761156 | c.1350G>C | synonymous_variant | 0.11 |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.1 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.1 |
rpoC | 764308 | c.939G>C | synonymous_variant | 0.1 |
rpoC | 764311 | c.942C>G | synonymous_variant | 0.11 |
rpoC | 764359 | c.990C>G | synonymous_variant | 0.11 |
rpoC | 764371 | c.1002G>C | synonymous_variant | 0.12 |
rpoC | 764377 | c.1008C>G | synonymous_variant | 0.12 |
rpoC | 764387 | c.1018_1020delTTGinsCTC | synonymous_variant | 0.12 |
rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.12 |
rpoC | 764428 | c.1059G>C | synonymous_variant | 0.14 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.12 |
rpoC | 764435 | c.1066A>C | synonymous_variant | 0.12 |
rpoC | 764441 | p.Ile358Leu | missense_variant | 0.13 |
rpoC | 764446 | c.1077T>C | synonymous_variant | 0.12 |
rpoC | 764449 | c.1080G>C | synonymous_variant | 0.12 |
rpoC | 764452 | c.1083T>C | synonymous_variant | 0.12 |
rpoC | 764458 | c.1089G>C | synonymous_variant | 0.13 |
rpoC | 764461 | c.1092A>G | synonymous_variant | 0.14 |
rpoC | 764485 | c.1116G>C | synonymous_variant | 0.14 |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.14 |
rpoC | 764498 | p.Ser377Ala | missense_variant | 0.14 |
rpoC | 764507 | p.Ala380Ser | missense_variant | 0.12 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.21 |
rpoC | 764539 | c.1170C>G | synonymous_variant | 0.23 |
rpoC | 764542 | c.1173C>G | synonymous_variant | 0.26 |
rpoC | 764548 | c.1179G>C | synonymous_variant | 0.24 |
rpoC | 764560 | c.1191T>C | synonymous_variant | 0.21 |
rpoC | 764575 | c.1206T>C | synonymous_variant | 0.16 |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.16 |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.17 |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.17 |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.17 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.19 |
rpoC | 764635 | c.1266C>G | synonymous_variant | 0.21 |
rpoC | 764650 | c.1281G>C | synonymous_variant | 0.25 |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.23 |
rpoC | 764668 | c.1299C>T | synonymous_variant | 0.2 |
rpoC | 764671 | c.1302G>C | synonymous_variant | 0.19 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.15 |
rpoC | 764706 | p.Leu446Gln | missense_variant | 0.15 |
rpoC | 764746 | c.1377G>T | synonymous_variant | 0.11 |
rpoC | 764749 | c.1380G>C | synonymous_variant | 0.16 |
rpoC | 764758 | c.1389C>G | synonymous_variant | 0.15 |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.14 |
rpoC | 764780 | c.1411_1412delAGinsTC | synonymous_variant | 0.11 |
rpoC | 764804 | p.Gln479Phe | missense_variant | 0.11 |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.12 |
rpoC | 764812 | c.1443C>G | synonymous_variant | 0.12 |
rpoC | 764815 | c.1446A>G | synonymous_variant | 0.12 |
rpoC | 764818 | c.1449G>C | synonymous_variant | 0.12 |
rpoC | 764824 | c.1455T>C | synonymous_variant | 0.12 |
rpoC | 764833 | c.1464A>G | synonymous_variant | 0.13 |
rpoC | 764843 | p.Ala492Thr | missense_variant | 0.14 |
rpoC | 764857 | c.1488G>C | synonymous_variant | 0.15 |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.15 |
rpoC | 764872 | c.1503A>C | synonymous_variant | 0.15 |
rpoC | 766174 | p.Asn935Lys | missense_variant | 0.1 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777416 | c.1065G>T | synonymous_variant | 0.92 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303807 | p.Gln293Lys | missense_variant | 0.11 |
fbiC | 1304159 | p.Val410Gly | missense_variant | 0.29 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473022 | n.1177G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473026 | n.1181T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476221 | n.2564T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476253 | n.2596A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476256 | n.2599A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476299 | n.2642C>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476308 | n.2651G>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.14 |
rpsA | 1833913 | p.Glu124Asp | missense_variant | 0.11 |
rpsA | 1833915 | p.Ala125Val | missense_variant | 0.11 |
rpsA | 1833920 | p.Lys127Glu | missense_variant | 0.11 |
rpsA | 1834303 | c.762T>G | synonymous_variant | 0.1 |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.11 |
rpsA | 1834307 | p.Asp256Gln | missense_variant | 0.11 |
rpsA | 1834327 | c.786G>C | synonymous_variant | 0.12 |
rpsA | 1834333 | p.Asp264Glu | missense_variant | 0.12 |
rpsA | 1834378 | c.837T>C | synonymous_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 |
PPE35 | 2168479 | p.Thr712Pro | missense_variant | 1.0 |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
folC | 2746543 | c.1056C>T | synonymous_variant | 0.11 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 |
Rv3083 | 3448954 | p.Pro151Thr | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568779 | c.-100T>C | upstream_gene_variant | 1.0 |
Rv3236c | 3612117 | p.Gly334Arg | missense_variant | 0.22 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 |
clpC1 | 4039898 | c.807C>G | synonymous_variant | 0.14 |
clpC1 | 4039904 | c.801A>G | synonymous_variant | 0.16 |
clpC1 | 4039916 | c.789T>C | synonymous_variant | 0.16 |
clpC1 | 4039922 | c.783C>T | synonymous_variant | 0.14 |
clpC1 | 4039929 | c.775_776delAGinsTC | synonymous_variant | 0.13 |
clpC1 | 4039931 | c.774T>C | synonymous_variant | 0.12 |
clpC1 | 4039934 | c.771G>C | synonymous_variant | 0.12 |
clpC1 | 4039940 | c.765G>C | synonymous_variant | 0.12 |
clpC1 | 4039943 | c.762G>C | synonymous_variant | 0.12 |
clpC1 | 4039946 | c.759A>C | synonymous_variant | 0.12 |
clpC1 | 4039949 | c.756G>C | synonymous_variant | 0.12 |
clpC1 | 4039952 | c.753T>C | synonymous_variant | 0.12 |
clpC1 | 4039960 | p.Thr249Ser | missense_variant | 0.13 |
clpC1 | 4039974 | p.Asp244Gly | missense_variant | 0.14 |
clpC1 | 4039977 | p.Lys243Arg | missense_variant | 0.14 |
clpC1 | 4039988 | c.717C>G | synonymous_variant | 0.14 |
clpC1 | 4039991 | c.714G>C | synonymous_variant | 0.14 |
clpC1 | 4039994 | p.Glu237Asp | missense_variant | 0.14 |
clpC1 | 4040001 | p.His235Arg | missense_variant | 0.13 |
clpC1 | 4040003 | p.Val234Asp | missense_variant | 0.13 |
clpC1 | 4040009 | c.696C>G | synonymous_variant | 0.13 |
clpC1 | 4040015 | c.690G>C | synonymous_variant | 0.12 |
clpC1 | 4040021 | c.684A>C | synonymous_variant | 0.12 |
clpC1 | 4040024 | c.681A>G | synonymous_variant | 0.12 |
clpC1 | 4040033 | c.672G>C | synonymous_variant | 0.11 |
clpC1 | 4040063 | c.642G>C | synonymous_variant | 0.12 |
clpC1 | 4040069 | c.636G>C | synonymous_variant | 0.12 |
embC | 4239973 | c.111T>G | synonymous_variant | 0.21 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4245764 | c.-750G>T | upstream_gene_variant | 0.15 |
embA | 4246329 | p.Thr1033Ala | missense_variant | 0.12 |
ubiA | 4269511 | p.Val108Gly | missense_variant | 0.31 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |