TB-Profiler result

Run: ERR2512606
Summary

Run ID: ERR2512606

Sample name:

Date: 31-03-2023 19:08:40

Number of reads: 935418

Percentage reads mapped: 77.62

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761109 p.Asp435Asn missense_variant 0.25 rifampicin
rpoB 761127 p.Ser441Ala missense_variant 0.24 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.14 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491259 c.477T>C synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761027 c.1221A>G synonymous_variant 0.13
rpoB 761030 c.1224G>T synonymous_variant 0.17
rpoB 761037 c.1231T>C synonymous_variant 0.2
rpoB 761051 c.1245G>C synonymous_variant 0.25
rpoB 761054 c.1248G>C synonymous_variant 0.24
rpoB 761057 c.1251G>C synonymous_variant 0.25
rpoB 761060 c.1254C>G synonymous_variant 0.25
rpoB 761084 c.1278C>A synonymous_variant 0.26
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.26
rpoB 761096 c.1290G>C synonymous_variant 0.25
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.25
rpoB 761102 c.1296A>G synonymous_variant 0.26
rpoB 761132 c.1326G>T synonymous_variant 0.23
rpoB 761133 c.1327T>C synonymous_variant 0.23
rpoB 761150 c.1344A>T synonymous_variant 0.19
rpoB 761159 c.1353G>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.21
rpoB 761180 c.1374A>C synonymous_variant 0.13
rpoB 762026 c.2220G>C synonymous_variant 0.13
rpoB 762050 c.2244G>A synonymous_variant 0.16
rpoB 762051 p.His749Tyr missense_variant 0.16
rpoB 762057 p.Ile751Val missense_variant 0.16
rpoB 762062 c.2256T>C synonymous_variant 0.19
rpoB 762065 c.2259T>C synonymous_variant 0.22
rpoB 762071 p.Asp755Glu missense_variant 0.24
rpoB 762080 c.2274G>C synonymous_variant 0.23
rpoB 762085 p.Ala760Glu missense_variant 0.27
rpoB 762089 c.2283G>A synonymous_variant 0.27
rpoB 762110 c.2304G>C synonymous_variant 0.24
rpoB 762114 p.Ile770Val missense_variant 0.24
rpoB 762122 p.Asp772Glu missense_variant 0.22
rpoB 762125 c.2319G>A synonymous_variant 0.22
rpoB 762126 p.Val774Ser missense_variant 0.23
rpoB 762134 c.2328C>A synonymous_variant 0.24
rpoB 762149 c.2343G>C synonymous_variant 0.24
rpoB 762156 p.Val784Ile missense_variant 0.24
rpoB 762167 c.2361T>C synonymous_variant 0.18
rpoB 762176 c.2370T>C synonymous_variant 0.11
rpoB 762177 p.Arg791Thr missense_variant 0.11
rpoB 762181 p.Asp792Ala missense_variant 0.1
rpoB 762185 c.2379G>C synonymous_variant 0.13
rpoB 762188 c.2382C>T synonymous_variant 0.13
rpoB 762194 c.2388G>C synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 763017 p.Gln1071Glu missense_variant 0.1
rpoC 763028 c.-342T>C upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763038 p.Thr1078Ala missense_variant 0.14
rpoC 763043 c.-327G>C upstream_gene_variant 0.14
rpoC 763053 c.-317T>C upstream_gene_variant 0.14
rpoC 763570 c.201G>C synonymous_variant 0.19
rpoC 763578 p.Phe70Tyr missense_variant 0.2
rpoC 763598 p.Arg77Lys missense_variant 0.22
rpoC 763606 c.237C>T synonymous_variant 0.17
rpoC 763615 c.246G>C synonymous_variant 0.15
rpoC 763618 c.249C>T synonymous_variant 0.15
rpoC 763622 p.Ala85Ser missense_variant 0.15
rpoC 763625 p.Lys86Arg missense_variant 0.14
rpoC 763630 c.261G>C synonymous_variant 0.14
rpoC 763633 c.264T>C synonymous_variant 0.14
rpoC 763642 c.273G>C synonymous_variant 0.16
rpoC 763648 c.279C>T synonymous_variant 0.19
rpoC 763657 p.Glu96Asp missense_variant 0.23
rpoC 763660 c.291T>G synonymous_variant 0.23
rpoC 763666 c.297G>C synonymous_variant 0.24
rpoC 763675 c.306C>G synonymous_variant 0.23
rpoC 763699 c.330G>T synonymous_variant 0.22
rpoC 763708 c.339G>C synonymous_variant 0.18
rpoC 763744 c.375G>C synonymous_variant 0.11
rpoC 763751 p.Ile128Val missense_variant 0.12
rpoC 763781 p.Ser138Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779311 p.Ile108Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305456 c.2526C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.29
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.36
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.42
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.71
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.73
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.76
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.75
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.84
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.83
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.8
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.76
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.79
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.72
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.5
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.43
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.43
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.38
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.45
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.49
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.73
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.61
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.16
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.62
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.59
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.47
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.17
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.61
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.46
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.62
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.62
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.62
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.79
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.74
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.9
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.74
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.88
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.15
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.14
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.84
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.7
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.73
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.86
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.82
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.84
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.87
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.73
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.73
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.86
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.8
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.84
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.8
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.88
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.88
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.89
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.86
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.89
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.82
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.85
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.82
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.82
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.86
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.79
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.8
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.82
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.77
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.72
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.73
rrs 1473289 n.1444_1445insTTTG non_coding_transcript_exon_variant 0.73
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.75
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.69
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.74
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.75
rrl 1473384 n.-274A>G upstream_gene_variant 0.65
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.5
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.6
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.57
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.57
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.57
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.57
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.43
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.43
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.57
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.43
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.5
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.75
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.8
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.6
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.8
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.8
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.8
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 0.33
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.75
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.8
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.75
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.9
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.71
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.57
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.67
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.8
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.43
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.83
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>T non_coding_transcript_exon_variant 0.29
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.24
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.25
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.2
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.24
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.19
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.24
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.18
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.22
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.16
rrl 1476303 n.2646T>C non_coding_transcript_exon_variant 0.16
rrl 1476307 n.2650A>C non_coding_transcript_exon_variant 0.17
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.16
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.72
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.72
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.63
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.57
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.48
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.18
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.27
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.45
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.38
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.48
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.42
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.29
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.19
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.25
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.25
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.12
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
rpsA 1834294 c.753G>C synonymous_variant 0.13
rpsA 1834298 p.Gln253Glu missense_variant 0.13
rpsA 1834306 c.765T>C synonymous_variant 0.14
rpsA 1834307 p.Asp256Gln missense_variant 0.14
rpsA 1834312 c.771G>A synonymous_variant 0.13
rpsA 1834327 c.786G>T synonymous_variant 0.18
rpsA 1834345 c.804C>T synonymous_variant 0.19
rpsA 1834348 c.807T>C synonymous_variant 0.17
rpsA 1834354 c.813G>C synonymous_variant 0.16
rpsA 1834357 c.816T>C synonymous_variant 0.15
rpsA 1834360 c.819G>C synonymous_variant 0.14
rpsA 1834361 c.820T>C synonymous_variant 0.13
rpsA 1834366 c.825A>G synonymous_variant 0.13
rpsA 1834375 c.834G>C synonymous_variant 0.13
rpsA 1834378 c.837T>C synonymous_variant 0.13
rpsA 1834387 c.846C>T synonymous_variant 0.16
rpsA 1834411 c.870T>C synonymous_variant 0.15
rpsA 1834417 c.876G>C synonymous_variant 0.12
rpsA 1834427 p.Ile296Val missense_variant 0.11
rpsA 1834435 c.894G>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155865 p.Val83Leu missense_variant 1.0
PPE35 2167745 c.2868C>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064830 c.1362C>T synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086891 c.72G>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4241613 p.Thr584Lys missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407797 p.Ser136Pro missense_variant 1.0