TB-Profiler result

Run: SRR6045036
Summary

Run ID: SRR6045036

Sample name:

Date: 04-04-2023 11:51:40

Number of reads: 78468

Percentage reads mapped: 13.35

Strain: lineage4;lineage3

Drug-resistance: Other

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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
lineage3 East-African-Indian CAS RD750 0.05
lineage4 Euro-American LAM;T;S;X;H None 0.95
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 1.0 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
gyrA 6481 c.-821G>T upstream_gene_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7772 c.471C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763172 c.-198G>T upstream_gene_variant 1.0
rpoC 765342 p.Pro658Leu missense_variant 0.5
rpoC 766772 p.Val1135Ile missense_variant 0.4
rpoC 767193 p.Thr1275Ile missense_variant 0.4
rpoC 767225 p.Pro1286Thr missense_variant 0.22
mmpL5 777100 p.Asp461Tyr missense_variant 1.0
mmpL5 777568 p.Gly305Ser missense_variant 1.0
mmpS5 778619 p.Ala96Glu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303650 c.720G>A synonymous_variant 0.29
Rv1258c 1407377 c.-37C>A upstream_gene_variant 1.0
embR 1416358 c.990C>A synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.67
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.67
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.89
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.89
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.93
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.93
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.93
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.96
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 1.0
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 1.0
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 1.0
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 1.0
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 1.0
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 1.0
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 1.0
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 1.0
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 1.0
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 1.0
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 1.0
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 1.0
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 1.0
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.84
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.95
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.95
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.95
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.95
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.95
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.96
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.96
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.96
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.96
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.9
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 1.0
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 1.0
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.86
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.8
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.8
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.44
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.8
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.8
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.8
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.6
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.4
rrs 1473054 n.1209C>T non_coding_transcript_exon_variant 0.4
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.5
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.5
rrs 1473131 n.1286G>T non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.71
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.71
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.71
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.71
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.71
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 1.0
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 1.0
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.93
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.96
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.94
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.94
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.94
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.94
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.94
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.94
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 1.0
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.92
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.92
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 1.0
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 1.0
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.92
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.92
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.92
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.92
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.75
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.67
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.92
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 1.0
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 1.0
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 1.0
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 1.0
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 1.0
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 1.0
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 1.0
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 1.0
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 1.0
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.8
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.8
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.62
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.62
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.88
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.88
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 1.0
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 1.0
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 1.0
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 1.0
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 1.0
rrl 1476213 n.2556G>A non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.56
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 1.0
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 1.0
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.95
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.95
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.95
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.95
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.95
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.95
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.95
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.96
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.96
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.96
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.98
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.99
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.99
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.98
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.98
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.98
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.98
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.99
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.99
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.99
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.99
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.99
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.98
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.95
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.92
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.88
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.88
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.88
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.88
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.88
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.88
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.88
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.88
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.88
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.94
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.93
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 0.83
inhA 1674642 p.Met147Ile missense_variant 0.5
rpsA 1834404 p.Ala288Val missense_variant 0.33
rpsA 1834732 c.1191T>C synonymous_variant 1.0
rpsA 1834733 p.Ala398Ser missense_variant 1.0
rpsA 1834753 c.1212T>C synonymous_variant 1.0
rpsA 1834765 p.Glu408Asp missense_variant 1.0
rpsA 1834775 p.Ala412Thr missense_variant 1.0
rpsA 1834780 c.1239A>G synonymous_variant 1.0
rpsA 1834786 c.1245A>G synonymous_variant 1.0
rpsA 1834789 c.1248T>C synonymous_variant 1.0
rpsA 1834792 c.1251G>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102862 p.Gly61Arg missense_variant 0.4
katG 2154991 p.Ser374Tyr missense_variant 0.5
katG 2155929 c.183G>A synonymous_variant 0.5
katG 2156301 c.-190G>T upstream_gene_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170371 p.Thr81Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726056 c.-137G>A upstream_gene_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746190 p.Gly470Val missense_variant 0.5
folC 2747464 c.135G>A synonymous_variant 0.33
Rv2752c 3065352 c.840A>G synonymous_variant 0.5
thyA 3073880 p.Glu198Lys missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087000 p.Ala61Thr missense_variant 1.0
fbiD 3339019 c.-99C>A upstream_gene_variant 0.5
fbiD 3339047 c.-71G>T upstream_gene_variant 0.33
Rv3083 3448526 p.Leu8Arg missense_variant 1.0
whiB7 3568857 c.-178C>T upstream_gene_variant 1.0
alr 3841082 c.339G>A synonymous_variant 0.5
rpoA 3877510 p.Glu333Gly missense_variant 0.5
rpoA 3877848 c.660C>T synonymous_variant 1.0
rpoA 3877875 c.633T>C synonymous_variant 0.5
rpoA 3877881 c.627G>C synonymous_variant 0.5
rpoA 3877887 c.621G>C synonymous_variant 0.5
rpoA 3877893 c.615C>T synonymous_variant 0.67
rpoA 3877900 p.Ser203Thr missense_variant 0.67
clpC1 4040741 c.-37G>C upstream_gene_variant 0.33
clpC1 4040898 c.-194C>T upstream_gene_variant 0.5
panD 4044023 c.259C>T synonymous_variant 1.0
embC 4240711 p.Trp283Cys missense_variant 0.29
embC 4241375 p.Ala505Ser missense_variant 0.67
embC 4241470 c.1608C>T synonymous_variant 0.67
embC 4241618 p.Trp586Arg missense_variant 1.0
embC 4241645 p.Gly595Trp missense_variant 0.4
embC 4241650 p.Leu596Phe missense_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 1.0
embB 4247163 p.Leu217Pro missense_variant 0.67
embB 4249606 c.3093C>T synonymous_variant 1.0
aftB 4267299 p.Pro513Gln missense_variant 0.5
ubiA 4269791 p.Ala15Ser missense_variant 0.5
ethR 4327843 p.Arg99Cys missense_variant 0.5
whiB6 4338378 p.Glu48Asp missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407913 p.Arg97His missense_variant 0.33
gid 4407918 c.285G>A synonymous_variant 0.33
gid 4408124 p.Ala27Ser missense_variant 0.4