TB-Profiler result

Run: ERR4132447
Summary

Run ID: ERR4132447

Sample name:

Date: 01-04-2023 04:30:27

Number of reads: 262894

Percentage reads mapped: 15.72

Strain: lineage4

Drug-resistance: HR-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
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.39 streptomycin
katG 2155168 p.Ser315Thr missense_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 6922 c.-380G>T upstream_gene_variant 0.25
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 8086 p.Asp262Val missense_variant 0.33
gyrA 8984 c.1683C>T synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575230 c.-118T>A upstream_gene_variant 0.4
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 0.29
ccsA 620744 c.857dupG frameshift_variant 0.17
rpoB 762901 p.Asp1032Gly missense_variant 0.15
rpoB 762935 p.Tyr1043* stop_gained 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765748 p.Tyr793* stop_gained 0.33
rpoC 765823 c.2454C>T synonymous_variant 0.25
rpoC 766823 p.Lys1152Glu missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775775 c.2706G>C synonymous_variant 0.33
mmpS5 778584 p.Asp108Asn missense_variant 0.5
mmpR5 779008 p.Val7Ile missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781770 p.Gly71Ser missense_variant 0.22
fbiC 1303880 p.Thr317Met missense_variant 0.29
fbiC 1304159 p.Val410Gly missense_variant 0.5
Rv1258c 1406298 c.1042delG frameshift_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.14
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.11
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.4
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.43
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.4
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.43
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.46
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.41
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.33
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.33
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.24
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.24
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.22
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.19
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.18
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.21
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.21
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.34
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.34
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.23
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.2
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.21
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.2
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.24
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.27
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.27
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.49
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.51
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.55
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.53
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.19
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.15
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.14
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.29
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.23
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.23
rrl 1473763 n.106C>A non_coding_transcript_exon_variant 0.18
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.17
rrl 1474255 n.598C>T non_coding_transcript_exon_variant 0.16
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.18
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.21
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.21
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.21
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.4
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.4
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.36
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.36
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.36
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.22
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.22
rrl 1475047 n.1390G>T non_coding_transcript_exon_variant 0.25
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.12
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.11
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.16
rrl 1475895 n.2238C>G non_coding_transcript_exon_variant 0.15
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.15
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.2
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.17
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.17
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.17
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.17
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.17
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.17
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.17
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.17
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.19
rrl 1476213 n.2556G>A non_coding_transcript_exon_variant 0.17
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.17
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.33
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.46
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.42
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.42
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.41
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.41
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.47
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.47
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.47
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.45
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.45
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.45
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.45
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.43
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.43
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.46
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.66
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.75
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.71
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.71
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.71
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.74
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.73
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.57
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.48
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.44
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.44
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.44
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.44
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.5
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.57
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.57
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.57
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.57
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.61
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.67
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.6
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.6
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.5
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.36
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.36
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.18
rrl 1476602 n.2945G>C non_coding_transcript_exon_variant 0.18
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.2
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2169386 c.1227C>A synonymous_variant 0.25
PPE35 2169394 p.Ala407Ser missense_variant 0.18
PPE35 2169397 p.Gly406Ser missense_variant 0.18
PPE35 2169581 c.1032C>G synonymous_variant 0.15
PPE35 2169587 c.1026G>A synonymous_variant 0.15
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2169728 c.885C>T synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.71
PPE35 2170415 c.198A>G synonymous_variant 0.2
PPE35 2170424 c.189G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289339 c.-98C>A upstream_gene_variant 0.29
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2725995 c.-198A>G upstream_gene_variant 0.4
ahpC 2726341 p.Val50Gly missense_variant 0.4
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2860602 c.-184A>C upstream_gene_variant 0.15
thyX 3067540 p.Ala136Thr missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087578 c.759A>T synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878424 c.84G>C synonymous_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4039786 p.Ile307Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245363 p.Phe711Leu missense_variant 0.29
embB 4247073 p.Gly187Glu missense_variant 0.67
embB 4248441 p.Thr643Ile missense_variant 1.0
embB 4249660 p.Met1049Ile missense_variant 0.25
ethR 4326961 c.-588G>C upstream_gene_variant 0.2
ethR 4326964 c.-585G>A upstream_gene_variant 0.2
ethR 4326970 c.-579G>T upstream_gene_variant 0.2
ethA 4327093 p.Ser127Arg missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0