TB-Profiler result

Run: SRR13861406
Summary

Run ID: SRR13861406

Sample name:

Date: 03-04-2023 09:30:55

Number of reads: 224204

Percentage reads mapped: 5.61

Strain: lineage4.9

Drug-resistance: MDR-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 0.4 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.76 streptomycin
katG 2155185 c.926_927insA frameshift_variant 1.0 isoniazid
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
gyrA 8396 p.Tyr365* stop_gained 1.0
fgd1 490821 p.Glu13Asp missense_variant 1.0
mshA 575959 p.Gln204His missense_variant 0.91
rpoB 761126 c.1320G>T synonymous_variant 0.4
rpoB 761129 c.1323G>C synonymous_variant 0.4
rpoB 761133 p.Leu443Ile missense_variant 0.4
rpoB 761150 c.1344A>C synonymous_variant 0.33
rpoB 761151 p.Leu449Val missense_variant 0.33
rpoB 761156 c.1350G>C synonymous_variant 0.33
rpoB 761162 c.1356G>C synonymous_variant 0.33
rpoB 761165 c.1359G>C synonymous_variant 0.33
rpoB 761168 c.1362C>G synonymous_variant 0.33
rpoB 761178 p.Ser458Thr missense_variant 0.4
rpoB 761192 c.1386C>G synonymous_variant 0.33
rpoB 761195 c.1389G>C synonymous_variant 0.33
rpoB 761196 p.Leu464Phe missense_variant 0.33
rpoB 761204 c.1398C>T synonymous_variant 0.29
rpoB 761207 c.1401C>T synonymous_variant 0.29
rpoB 761220 p.Ser472Thr missense_variant 0.33
rpoB 761234 c.1428G>C synonymous_variant 0.4
rpoB 761235 p.Met477Val missense_variant 0.33
rpoC 764401 c.1032C>T synonymous_variant 0.2
rpoC 764404 c.1035C>T synonymous_variant 0.2
rpoC 764405 c.1036A>C synonymous_variant 0.2
rpoC 764419 c.1050C>T synonymous_variant 0.22
rpoC 764428 c.1059G>T synonymous_variant 0.25
rpoC 764434 c.1065A>G synonymous_variant 0.22
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.25
rpoC 764441 p.Ile358Leu missense_variant 0.22
rpoC 764446 c.1077T>C synonymous_variant 0.25
rpoC 764451 p.Gly361Ala missense_variant 0.22
rpoC 764461 p.Glu364Asp missense_variant 0.2
rpoC 764470 c.1101C>G synonymous_variant 0.2
rpoC 764471 p.Asn368Arg missense_variant 0.2
rpoC 764479 c.1110G>A synonymous_variant 0.18
rpoC 764485 c.1116G>C synonymous_variant 0.2
rpoC 764498 p.Ser377Ala missense_variant 0.2
rpoC 764503 c.1134G>C synonymous_variant 0.18
rpoC 764509 c.1140G>C synonymous_variant 0.18
rpoC 764513 p.Phe382Leu missense_variant 0.18
rpoC 766364 p.Ala999Ser missense_variant 1.0
mmpL5 775945 p.Val846Leu missense_variant 1.0
mmpL5 776248 p.Ala745Pro missense_variant 0.4
mmpL5 778345 p.Leu46Ile missense_variant 1.0
mmpL5 778992 c.-512C>T upstream_gene_variant 1.0
mmpR5 779231 p.Glu81Val missense_variant 1.0
fbiC 1303186 p.Tyr86His missense_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.22
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.4
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.4
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.71
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.77
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.71
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.83
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.83
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.84
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.84
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.84
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.8
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.77
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.77
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.77
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.77
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.77
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.77
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.77
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.27
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.75
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.74
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.76
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.68
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.6
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.47
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.47
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.21
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.2
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.21
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.29
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.68
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.7
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.69
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.7
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.7
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.72
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.72
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.72
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.72
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.74
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.74
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.68
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.69
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.77
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.79
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.82
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.8
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.8
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.8
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.82
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.78
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.78
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.79
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.8
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.8
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.53
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.4
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.54
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.5
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.5
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.5
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.47
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.47
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.47
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.47
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.47
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.47
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.5
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.54
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.54
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.54
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.43
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.84
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.88
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.93
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.93
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.93
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.93
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.93
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.93
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.91
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.93
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.93
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.93
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.91
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.91
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.91
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.92
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.92
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.92
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.93
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.91
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.98
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.98
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.89
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.97
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.79
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.97
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.97
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.97
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.98
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.9
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.92
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.9
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.87
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.89
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.89
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.89
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.89
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.9
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.9
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.9
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.92
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.9
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.86
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.86
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.86
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.8
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.31
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.21
fabG1 1673157 c.-283G>C upstream_gene_variant 1.0
ndh 2101749 p.Thr432Ser missense_variant 1.0
katG 2155982 p.Asn44His missense_variant 1.0
PPE35 2168042 c.2571G>C synonymous_variant 1.0
PPE35 2169365 c.1248C>T synonymous_variant 1.0
thyX 3067878 p.Val23Gly missense_variant 1.0
fbiD 3339188 p.Thr24Ser missense_variant 1.0
fprA 3474999 c.993G>T synonymous_variant 1.0
whiB7 3568496 p.Pro62Ser missense_variant 1.0
Rv3236c 3612323 p.Pro265Gln missense_variant 1.0
fbiB 3641121 c.-414C>A upstream_gene_variant 1.0
clpC1 4038346 p.Glu787* stop_gained 1.0
embC 4239894 p.Ala11Gly missense_variant 1.0
ethA 4327073 p.Leu134Pro missense_variant 1.0