TB-Profiler result

Run: SRR13861232
Summary

Run ID: SRR13861232

Sample name:

Date: 03-04-2023 09:26:43

Number of reads: 441798

Percentage reads mapped: 7.37

Strain: lineage4.9

Drug-resistance: RR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761131 p.Gly442Glu missense_variant 0.13 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.71 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6667 p.Gln476His missense_variant 1.0
gyrA 7289 c.-13_-12insT upstream_gene_variant 1.0
rpoB 760214 p.Asn136Lys missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.13
rpoB 761129 c.1323G>C synonymous_variant 0.13
rpoB 761133 p.Leu443Ile missense_variant 0.12
rpoB 761150 c.1344A>C synonymous_variant 0.12
rpoB 761151 p.Leu449Val missense_variant 0.12
rpoB 761156 c.1350G>C synonymous_variant 0.12
rpoB 761162 c.1356G>C synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.12
rpoB 761168 c.1362C>G synonymous_variant 0.12
rpoB 761178 p.Ser458Thr missense_variant 0.12
rpoB 761192 c.1386C>G synonymous_variant 0.13
rpoB 761195 c.1389G>C synonymous_variant 0.12
rpoB 761196 p.Leu464Phe missense_variant 0.12
rpoB 761204 c.1398C>T synonymous_variant 0.13
rpoB 761207 c.1401C>T synonymous_variant 0.12
rpoB 761213 c.1407G>A synonymous_variant 0.13
rpoB 761220 p.Ser472Thr missense_variant 0.17
rpoB 761234 c.1428G>C synonymous_variant 0.14
rpoB 761235 p.Met477Val missense_variant 0.14
rpoC 764428 c.1059G>T synonymous_variant 0.13
rpoC 764434 c.1065A>G synonymous_variant 0.13
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.13
rpoC 764441 p.Ile358Leu missense_variant 0.14
rpoC 764446 c.1077T>C synonymous_variant 0.14
rpoC 764451 p.Gly361Ala missense_variant 0.14
rpoC 764461 p.Glu364Asp missense_variant 0.12
rpoC 764470 c.1101C>G synonymous_variant 0.12
rpoC 764471 p.Asn368Arg missense_variant 0.12
rpoC 764479 c.1110G>A synonymous_variant 0.12
rpoC 764485 c.1116G>C synonymous_variant 0.12
rpoC 764498 p.Ser377Ala missense_variant 0.13
rpoC 764503 c.1134G>C synonymous_variant 0.13
rpoC 764509 c.1140G>C synonymous_variant 0.13
rpoC 764513 p.Phe382Leu missense_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.15
fbiC 1304005 p.Pro359Ser missense_variant 1.0
rrs 1471943 n.98T>C non_coding_transcript_exon_variant 1.0
rrs 1472075 n.230A>C non_coding_transcript_exon_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.16
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.39
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.39
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.57
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.63
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.42
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.65
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.65
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.65
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.65
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.65
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.73
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.73
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.7
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.69
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.69
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.69
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.74
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.19
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.73
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.73
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.72
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.42
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.33
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.28
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.13
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.4
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.6
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.6
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.61
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.6
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.58
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.57
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.6
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.57
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.57
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.57
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.58
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.58
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.57
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.57
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.69
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.7
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.79
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.73
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.74
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.74
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.72
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.68
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.69
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.66
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.67
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.71
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.71
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.46
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.17
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.16
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.17
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.17
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.17
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.31
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.23
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.21
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.21
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.21
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.15
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.15
rrs 1473066 n.1221A>T non_coding_transcript_exon_variant 1.0
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.42
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.48
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.48
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.48
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.48
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.48
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.48
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.43
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.42
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.42
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.46
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.42
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.43
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.43
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.45
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.42
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.37
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.37
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.34
rrs 1473370 n.1525T>C non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.14
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.73
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.75
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.81
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.79
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.8
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.78
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.79
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.78
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.79
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.79
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.8
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.82
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.8
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.81
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.82
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.82
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.83
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.85
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.87
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.95
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.86
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.74
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.95
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.95
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.86
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.95
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.96
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.89
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.91
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.89
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.87
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.87
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.87
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.87
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.86
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.86
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.86
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.86
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.86
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.87
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.87
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.87
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.87
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.84
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.43
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.27
fabG1 1673813 p.Arg125Leu missense_variant 1.0
inhA 1674784 p.Arg195Gly missense_variant 1.0
ndh 2101793 p.Trp417* stop_gained 1.0
PPE35 2169624 p.Gly330Asp missense_variant 1.0
kasA 2519223 p.Thr370Ile missense_variant 1.0
ahpC 2726213 c.21C>T synonymous_variant 1.0
ribD 2987016 p.Gly60Arg missense_variant 1.0
Rv2752c 3065644 p.Thr183Ser missense_variant 1.0
thyA 3074595 c.-124C>A upstream_gene_variant 1.0
alr 3841581 c.-161T>A upstream_gene_variant 1.0
embC 4242810 p.Leu983Gln missense_variant 1.0
embB 4246553 p.Arg14Trp missense_variant 1.0
embB 4248920 p.Val803Met missense_variant 0.95
embB 4249551 p.Arg1013Leu missense_variant 1.0
ethA 4326296 p.Leu393Gln missense_variant 1.0