TB-Profiler result

Run: ERR2514137
Summary

Run ID: ERR2514137

Sample name:

Date: 31-03-2023 20:08:25

Number of reads: 602483

Percentage reads mapped: 88.35

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 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.48 streptomycin
katG 2155129 p.Trp328Leu missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 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
gyrB 7199 p.Glu654Lys missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9818 c.2517A>G splice_region_variant&stop_retained_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575972 p.Glu209Lys missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760309 p.Val168Ala missense_variant 1.0
rpoB 761054 c.1248G>C synonymous_variant 0.12
rpoB 761058 p.Val418Thr missense_variant 0.12
rpoB 761084 c.1278C>A synonymous_variant 0.12
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.12
rpoB 761102 c.1296A>G synonymous_variant 0.1
rpoB 762879 p.Met1025Leu missense_variant 0.15
rpoC 762902 c.-468C>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764461 c.1092A>G synonymous_variant 0.12
rpoC 764485 c.1116G>C synonymous_variant 0.11
rpoC 764491 c.1122G>C synonymous_variant 0.11
rpoC 764497 c.1128A>G synonymous_variant 0.1
rpoC 764498 p.Ser377Ala missense_variant 0.11
rpoC 764503 c.1134G>C synonymous_variant 0.12
rpoC 764507 p.Ala380Ser missense_variant 0.12
rpoC 764545 c.1176C>G synonymous_variant 0.11
rpoC 764548 c.1179G>T synonymous_variant 0.11
rpoC 764551 c.1182G>C synonymous_variant 0.12
rpoC 764566 c.1197C>G synonymous_variant 0.11
rpoC 764665 c.1296C>G synonymous_variant 0.1
rpoC 764671 c.1302G>C synonymous_variant 0.1
rpoC 764703 p.Lys445Ser missense_variant 0.1
rpoC 764706 p.Leu446Gln missense_variant 0.11
rpoC 764713 c.1344G>C synonymous_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775689 c.2791delG frameshift_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778588 p.Gln106His missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.22
rrs 1472114 n.269A>G non_coding_transcript_exon_variant 0.2
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.2
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.2
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.45
rrs 1472151 n.306C>G non_coding_transcript_exon_variant 0.42
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.45
rrs 1472188 n.343A>G non_coding_transcript_exon_variant 0.43
rrs 1472207 n.362A>G non_coding_transcript_exon_variant 0.43
rrs 1472208 n.363A>G non_coding_transcript_exon_variant 0.43
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.43
rrs 1472244 n.399C>T non_coding_transcript_exon_variant 0.43
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.57
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.43
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.43
rrs 1472274 n.429A>G non_coding_transcript_exon_variant 0.6
rrs 1472507 n.662C>G 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 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.8
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.91
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.91
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.71
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.29
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.71
rrs 1472687 n.842A>C non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 1.0
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.44
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.44
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.44
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.57
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.48
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.61
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.24
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.56
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.43
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.57
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.57
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.75
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.67
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.75
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.75
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.75
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.75
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.6
rrs 1472988 n.1143T>G non_coding_transcript_exon_variant 0.5
rrs 1473001 n.1156G>A non_coding_transcript_exon_variant 0.25
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.25
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.25
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.17
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.25
rrs 1473017 n.1172A>G non_coding_transcript_exon_variant 0.15
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.64
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.4
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.6
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.73
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.79
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.5
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.79
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.33
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.42
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.75
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.3
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.7
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.7
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.3
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.7
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.56
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.38
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.38
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.5
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.5
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.5
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.4
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.4
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.4
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1475692 n.2035G>C non_coding_transcript_exon_variant 0.67
rrl 1475695 n.2038G>C non_coding_transcript_exon_variant 0.67
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 1.0
rrl 1475704 n.2047C>G non_coding_transcript_exon_variant 0.67
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 1.0
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.67
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 1.0
rrl 1475759 n.2102C>G non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.5
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.5
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.5
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.8
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.3
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3
rrl 1476458 n.2801T>C non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
fabG1 1673402 c.-38A>G upstream_gene_variant 0.1
inhA 1674833 p.Ala211Val missense_variant 0.22
rpsA 1833364 c.-178C>A upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155122 c.990C>T synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169079 c.1533dupG frameshift_variant 0.12
PPE35 2169706 p.Gly303Arg missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518598 p.Ala162Thr missense_variant 0.12
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518609 p.Met165Ile missense_variant 0.12
kasA 2518889 p.Ala259Thr missense_variant 0.11
kasA 2518947 p.Val278Ala missense_variant 0.11
eis 2714569 p.Ala255Gly missense_variant 0.25
folC 2746800 p.Arg267Trp missense_variant 0.14
folC 2747158 c.441G>C synonymous_variant 0.11
pepQ 2860251 c.168C>T synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449096 p.Gly198Asp missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612831 p.Asp96Asn missense_variant 0.17
Rv3236c 3613279 c.-163C>T upstream_gene_variant 0.11
rpoA 3877991 p.Lys173Glu missense_variant 0.11
ddn 3986705 c.-138delA upstream_gene_variant 0.14
clpC1 4039067 c.1638G>A synonymous_variant 0.15
clpC1 4039455 p.Ala417Val missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249330 p.Met939Ile missense_variant 0.23
aftB 4267499 c.1337delC frameshift_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268354 c.483G>A synonymous_variant 0.17
aftB 4268518 p.Ala107Thr missense_variant 0.11
ubiA 4269322 p.Pro171Leu missense_variant 0.15
ubiA 4269859 c.-26A>C upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407640 p.Val188Glu missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0