TB-Profiler result

Run: SRR10315701
Summary

Run ID: SRR10315701

Sample name:

Date: 02-04-2023 17:16:13

Number of reads: 5692158

Percentage reads mapped: 48.43

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rrs 1472753 n.908A>G non_coding_transcript_exon_variant 0.36 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.99 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
mshA 576108 p.Ala254Gly missense_variant 0.34
rpoB 761547 p.Val581Met missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.13
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.24
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.49
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.49
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.5
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.51
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.51
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.53
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.52
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.51
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.51
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.5
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.49
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.49
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.47
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.43
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.42
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.43
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.4
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.42
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.43
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.45
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.44
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.45
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.47
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.49
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.57
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.67
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.65
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.66
rrs 1472669 n.824_825insTGG non_coding_transcript_exon_variant 0.54
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.52
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.51
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.56
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.57
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.53
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.58
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.58
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.59
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.57
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.57
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.6
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.3
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.15
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.51
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.52
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.53
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.52
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.52
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.55
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.53
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.51
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.51
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.51
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.51
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.51
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.51
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.51
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.51
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.5
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.52
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.56
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.36
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.42
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.25
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.1
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.12
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.13
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.1
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.11
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476128 n.2471T>A non_coding_transcript_exon_variant 0.16
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.27
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.37
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.5
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.59
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.58
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.6
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.59
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.59
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.61
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.6
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.59
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.59
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.6
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.62
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.63
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.72
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.73
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.83
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.79
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.71
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.71
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.71
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.71
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.7
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.7
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.7
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.72
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.72
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.72
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.79
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.8
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.83
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.83
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.84
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.82
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.78
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.81
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.8
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.68
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.55
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.54
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.5
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.33
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.47
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.47
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.45
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.47
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.46
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.46
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.45
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.41
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.36
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.22
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288864 p.Asp126Glu missense_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0