TB-Profiler result

Run: ERR4821176
Summary

Run ID: ERR4821176

Sample name:

Date: 01-04-2023 17:06:13

Number of reads: 716236

Percentage reads mapped: 88.34

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
gyrA 7572 p.Ser91Ala missense_variant 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761127 p.Ser441Ala missense_variant 0.11 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.12 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.23 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.29 streptomycin
embB 4247622 p.Leu370Arg missense_variant 1.0 ethambutol
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
gyrB 6458 p.Val407Met missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7547 c.246C>T synonymous_variant 0.17
gyrA 7559 c.258G>T synonymous_variant 0.14
gyrA 7571 c.270G>C synonymous_variant 0.13
gyrA 7584 p.Ser95Ala missense_variant 0.11
gyrA 7589 c.288G>C synonymous_variant 0.11
gyrA 7591 p.Val97Ala missense_variant 0.11
gyrA 7596 p.Met99Leu missense_variant 0.12
gyrA 7600 p.Ala100Val missense_variant 0.12
gyrA 7625 c.324G>C synonymous_variant 0.11
gyrA 7628 c.327G>C synonymous_variant 0.11
gyrA 7631 c.330G>C synonymous_variant 0.11
gyrA 7633 p.Asp111Ala missense_variant 0.11
gyrA 7643 c.342C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490928 p.Gly49Asp missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759686 c.-121G>T upstream_gene_variant 0.22
rpoB 761132 c.1326G>C synonymous_variant 0.11
rpoB 761133 c.1327T>C synonymous_variant 0.11
rpoB 761150 c.1344A>C synonymous_variant 0.11
rpoB 761159 c.1353G>C synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.12
rpoB 761174 c.1368T>C synonymous_variant 0.12
rpoB 761180 c.1374A>C synonymous_variant 0.11
rpoB 761183 c.1377T>C synonymous_variant 0.12
rpoB 761186 p.Glu460Asp missense_variant 0.12
rpoB 761189 c.1383T>C synonymous_variant 0.12
rpoB 761192 c.1386C>G synonymous_variant 0.12
rpoB 761195 c.1389G>C synonymous_variant 0.12
rpoB 761201 c.1395G>A synonymous_variant 0.11
rpoB 761207 c.1401C>A synonymous_variant 0.12
rpoB 761213 c.1407G>C synonymous_variant 0.12
rpoB 761219 c.1413G>C synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763043 c.-327G>C upstream_gene_variant 0.14
rpoC 763053 c.-317T>C upstream_gene_variant 0.13
rpoB 763078 p.Val1091Ala missense_variant 0.11
rpoC 763115 c.-255T>C upstream_gene_variant 0.1
rpoC 763642 c.273G>C synonymous_variant 0.12
rpoC 763657 p.Glu96Asp missense_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.13
rpoC 763666 c.297G>C synonymous_variant 0.14
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763699 c.330G>T synonymous_variant 0.14
rpoC 763708 c.339G>C synonymous_variant 0.12
rpoC 764353 c.984G>T synonymous_variant 0.12
rpoC 764359 c.990C>G synonymous_variant 0.18
rpoC 764371 c.1002G>T synonymous_variant 0.18
rpoC 764377 c.1008C>G synonymous_variant 0.16
rpoC 764380 c.1011G>C synonymous_variant 0.16
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.16
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.16
rpoC 764410 c.1041G>C synonymous_variant 0.15
rpoC 764424 p.Asn352Thr missense_variant 0.18
rpoC 764428 c.1059G>A synonymous_variant 0.18
rpoC 764431 c.1062G>C synonymous_variant 0.18
rpoC 764434 c.1065A>G synonymous_variant 0.18
rpoC 764435 c.1066_1068delAGGinsCGA synonymous_variant 0.18
rpoC 764441 p.Ile358Leu missense_variant 0.17
rpoC 764446 p.Asp359Glu missense_variant 0.16
rpoC 764452 c.1083T>C synonymous_variant 0.16
rpoC 764455 c.1086G>C synonymous_variant 0.15
rpoC 764458 c.1089G>C synonymous_variant 0.18
rpoC 764461 c.1092A>G synonymous_variant 0.18
rpoC 764485 c.1116G>C synonymous_variant 0.27
rpoC 764491 c.1122G>T synonymous_variant 0.29
rpoC 764503 c.1134G>T synonymous_variant 0.21
rpoC 764509 c.1140G>C synonymous_variant 0.23
rpoC 764512 c.1143G>C synonymous_variant 0.19
rpoC 764530 c.1161C>T synonymous_variant 0.2
rpoC 764536 c.1167G>C synonymous_variant 0.21
rpoC 764543 p.Thr392Ala missense_variant 0.19
rpoC 764548 c.1179G>C synonymous_variant 0.18
rpoC 764551 c.1182G>C synonymous_variant 0.16
rpoC 764573 p.Leu402Ile missense_variant 0.2
rpoC 764578 c.1209C>G synonymous_variant 0.2
rpoC 764581 c.1212T>C synonymous_variant 0.19
rpoC 764582 p.Leu405Met missense_variant 0.18
rpoC 764602 c.1233C>T synonymous_variant 0.21
rpoC 764605 c.1236G>T synonymous_variant 0.21
rpoC 764611 c.1242G>T synonymous_variant 0.2
rpoC 764632 c.1263T>A synonymous_variant 0.12
rpoC 764647 c.1278C>T synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764653 c.1284G>C synonymous_variant 0.13
rpoC 764656 c.1287C>T synonymous_variant 0.13
rpoC 764662 c.1293G>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776682 p.Leu600Pro missense_variant 0.11
mmpL5 777189 p.Tyr431Cys missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.4
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.81
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.59
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.54
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.54
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.83
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.54
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.36
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.59
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.67
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.43
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.57
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.75
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.75
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.38
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.38
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.43
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.59
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.94
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.77
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.14
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.65
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.85
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.69
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.64
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.17
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.38
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.19
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.63
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.23
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.3
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.12
rrs 1472787 n.942A>G non_coding_transcript_exon_variant 0.12
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.59
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.2
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.14
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.6
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.6
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.6
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.92
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.29
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.62
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.29
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.96
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.92
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.72
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.26
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.26
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.83
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.52
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.56
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.77
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.83
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.88
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.62
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.66
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.89
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.86
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.85
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.82
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.85
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.85
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.85
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.2
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.85
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.64
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.61
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.9
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.89
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.77
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.74
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.83
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.84
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.83
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.84
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.7
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.66
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.59
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.71
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.75
rrl 1474643 n.986A>G non_coding_transcript_exon_variant 1.0
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 1.0
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 1.0
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 1.0
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 1.0
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 1.0
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 1.0
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 1.0
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 1.0
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.91
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.89
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.93
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.4
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.33
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.33
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.33
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.29
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.29
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.29
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.29
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.29
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.29
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.2
rpsA 1833844 c.303C>A synonymous_variant 0.11
rpsA 1833970 c.429G>T synonymous_variant 0.11
rpsA 1833991 c.450C>T synonymous_variant 0.11
rpsA 1834009 c.468C>T synonymous_variant 0.14
rpsA 1834040 p.Lys167Arg missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834195 c.654G>C synonymous_variant 0.17
rpsA 1834234 c.693G>C synonymous_variant 0.24
rpsA 1834240 c.699T>C synonymous_variant 0.18
rpsA 1834246 c.705G>T synonymous_variant 0.2
rpsA 1834249 c.708T>C synonymous_variant 0.19
rpsA 1834258 c.717G>A synonymous_variant 0.17
rpsA 1834261 c.720A>G synonymous_variant 0.16
rpsA 1834264 c.723G>C synonymous_variant 0.16
rpsA 1834294 c.753G>C synonymous_variant 0.18
rpsA 1834298 p.Gln253Glu missense_variant 0.18
rpsA 1834306 c.765T>C synonymous_variant 0.2
rpsA 1834307 p.Asp256Gln missense_variant 0.17
rpsA 1834312 c.771G>A synonymous_variant 0.17
rpsA 1834327 c.786G>T synonymous_variant 0.19
rpsA 1834345 c.804C>T synonymous_variant 0.11
rpsA 1834387 c.846C>T synonymous_variant 0.13
rpsA 1834411 c.870T>C synonymous_variant 0.12
rpsA 1834417 c.876G>C synonymous_variant 0.13
rpsA 1834423 c.882G>C synonymous_variant 0.14
rpsA 1834427 p.Ile296Val missense_variant 0.1
rpsA 1834435 c.894G>C synonymous_variant 0.1
rpsA 1834451 c.910T>C synonymous_variant 0.14
rpsA 1834861 c.1320G>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155124 p.Asn330Asp missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169821 c.792C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519320 p.Phe402Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613293 c.-177G>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4266972 p.Gly622Asp missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268746 p.Gly31* stop_gained 0.17
ethA 4326676 p.Ser266Arg missense_variant 1.0
ethA 4327181 p.Ile98Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407927 p.Glu92Asp missense_variant 1.0