TB-Profiler result

Run: ERR4831529
Summary

Run ID: ERR4831529

Sample name:

Date: 01-04-2023 20:59:33

Number of reads: 1132552

Percentage reads mapped: 15.45

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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.17 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.22 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 0.96 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 1.0 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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.13
ccsA 619971 c.81C>T synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 0.93
rpoB 761183 c.1377T>C synonymous_variant 0.1
rpoB 761189 c.1383T>C synonymous_variant 0.11
rpoB 761195 c.1389G>C synonymous_variant 0.17
rpoB 761201 c.1395G>A synonymous_variant 0.16
rpoB 761213 c.1407G>C synonymous_variant 0.2
rpoB 761218 p.Pro471His missense_variant 0.17
rpoB 761222 c.1416G>C synonymous_variant 0.17
rpoB 761228 c.1422C>T synonymous_variant 0.17
rpoB 761249 c.1443A>G synonymous_variant 0.18
rpoB 761252 c.1446C>G synonymous_variant 0.18
rpoB 761255 c.1449T>G synonymous_variant 0.19
rpoB 761261 c.1455G>A synonymous_variant 0.14
rpoB 761264 c.1458C>G synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763486 c.117T>C synonymous_variant 0.47
rpoC 763498 c.129G>A synonymous_variant 0.45
rpoC 763501 p.Asp44Glu missense_variant 0.45
rpoC 763504 c.135C>T synonymous_variant 0.46
rpoC 763507 c.138G>C synonymous_variant 0.45
rpoC 763528 c.159G>A synonymous_variant 0.45
rpoC 763534 c.165T>C synonymous_variant 0.47
rpoC 763535 p.Arg56Lys missense_variant 0.47
rpoC 763546 c.177A>G synonymous_variant 0.45
rpoC 763550 p.Tyr61His missense_variant 0.47
rpoC 763555 c.186C>T synonymous_variant 0.41
rpoC 763570 c.201G>C synonymous_variant 0.62
rpoC 763578 p.Phe70Tyr missense_variant 0.5
rpoC 763582 c.213G>A synonymous_variant 0.46
rpoC 763586 p.Ile73Val missense_variant 0.43
rpoC 763589 p.Ile74Val missense_variant 0.45
rpoC 763597 p.Glu76Asp missense_variant 0.49
rpoC 763609 c.240C>A synonymous_variant 0.47
rpoC 763612 c.243G>A synonymous_variant 0.46
rpoC 763615 c.246G>C synonymous_variant 0.48
rpoC 763618 c.249C>T synonymous_variant 0.46
rpoC 763627 c.258G>A synonymous_variant 0.45
rpoC 763630 c.261G>C synonymous_variant 0.46
rpoC 763633 c.264T>C synonymous_variant 0.46
rpoC 763636 c.267T>C synonymous_variant 0.45
rpoC 763651 c.282C>T synonymous_variant 0.14
rpoC 764428 c.1059G>T synonymous_variant 0.17
rpoC 764434 c.1065A>G synonymous_variant 0.18
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.18
rpoC 764441 p.Ile358Leu missense_variant 0.18
rpoC 764446 c.1077T>C synonymous_variant 0.21
rpoC 764449 c.1080G>T synonymous_variant 0.2
rpoC 764452 c.1083T>C synonymous_variant 0.18
rpoC 764461 p.Glu364Asp missense_variant 0.19
rpoC 764464 c.1095C>T synonymous_variant 0.19
rpoC 764470 c.1101C>A synonymous_variant 0.14
rpoC 764471 p.Asn368Gln missense_variant 0.14
rpoC 764498 p.Ser377Ala missense_variant 0.35
rpoC 764503 c.1134G>C synonymous_variant 0.38
rpoC 764506 c.1137C>T synonymous_variant 0.33
rpoC 764509 c.1140G>C synonymous_variant 0.33
rpoC 764512 c.1143G>C synonymous_variant 0.33
rpoC 764513 p.Phe382Ile missense_variant 0.33
rpoC 764521 c.1152T>C synonymous_variant 0.3
rpoC 764536 c.1167G>T synonymous_variant 0.35
rpoC 764539 c.1170C>G synonymous_variant 0.38
rpoC 764548 c.1179G>A synonymous_variant 0.35
rpoC 764566 c.1197C>G synonymous_variant 0.25
rpoC 764572 c.1203G>C synonymous_variant 0.18
rpoC 764644 c.1275G>C synonymous_variant 0.27
rpoC 764650 c.1281G>T synonymous_variant 0.28
rpoC 764656 c.1287C>T synonymous_variant 0.32
rpoC 764662 c.1293G>C synonymous_variant 0.31
rpoC 764672 p.Gln435Asn missense_variant 0.33
rpoC 764677 c.1308C>G synonymous_variant 0.32
rpoC 764681 p.Leu438Met missense_variant 0.3
rpoC 764684 p.His439Tyr missense_variant 0.31
rpoC 764689 c.1320G>A synonymous_variant 0.32
rpoC 764698 c.1329G>T synonymous_variant 0.33
rpoC 764701 c.1332C>G synonymous_variant 0.35
rpoC 764705 p.Leu446Glu missense_variant 0.35
rpoC 764731 c.1362G>T synonymous_variant 0.21
rpoC 764737 c.1368G>C synonymous_variant 0.14
rpoC 764819 p.Trp484Gly missense_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
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 1472570 n.725G>A non_coding_transcript_exon_variant 0.11
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.32
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.31
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.31
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.3
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.32
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.42
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.39
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.37
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.37
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.32
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.36
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.29
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.28
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.22
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.19
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.34
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.84
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.85
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.85
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.85
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.85
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.85
rrs 1473094 n.1249T>C non_coding_transcript_exon_variant 0.85
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.85
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.84
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.84
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.83
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.84
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.57
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.41
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.41
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.41
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.42
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.42
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.43
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.43
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.44
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.45
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.42
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.39
rrl 1473731 n.74T>G non_coding_transcript_exon_variant 0.13
rrl 1473746 n.90delC non_coding_transcript_exon_variant 0.15
rrl 1473750 n.93C>G non_coding_transcript_exon_variant 0.16
rrl 1473752 n.95G>A non_coding_transcript_exon_variant 0.15
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.16
rrl 1473765 n.108A>G non_coding_transcript_exon_variant 0.16
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.14
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.16
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.13
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.14
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.15
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.15
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.18
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.19
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.19
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.19
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.24
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.24
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.51
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.28
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.59
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.6
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.61
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.62
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.57
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.57
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.54
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.52
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.55
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.56
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.54
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.52
inhA 1674952 p.Pro251Ala missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918582 p.Ala215Thr missense_variant 0.12
katG 2153933 p.Ala727Ser missense_variant 0.35
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155139 p.Pro325Ser missense_variant 1.0
katG 2155698 c.414C>T synonymous_variant 0.12
katG 2155997 p.Trp39Arg missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.28
PPE35 2169866 c.747G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.13
thyX 3067431 p.Arg172His missense_variant 0.13
thyA 3073806 c.666C>G synonymous_variant 0.15
thyA 3074394 c.78C>A synonymous_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 0.93
rpoA 3878641 c.-134C>G upstream_gene_variant 0.15
clpC1 4038795 p.Ser637Ile missense_variant 0.14
clpC1 4038803 p.Ile634Val missense_variant 0.14
clpC1 4038806 c.1899G>A synonymous_variant 0.15
clpC1 4038810 p.Gln632Pro missense_variant 0.24
clpC1 4038835 p.Phe624Leu missense_variant 0.32
clpC1 4038839 c.1866G>C synonymous_variant 0.32
clpC1 4038842 c.1863G>C synonymous_variant 0.3
clpC1 4038845 c.1860G>C synonymous_variant 0.3
clpC1 4038849 p.Phe619Tyr missense_variant 0.3
clpC1 4038860 c.1845G>C synonymous_variant 0.5
clpC1 4038875 c.1830C>G synonymous_variant 0.38
clpC1 4038878 c.1827A>G synonymous_variant 0.43
clpC1 4038890 c.1815G>A synonymous_variant 0.32
clpC1 4038893 c.1812C>T synonymous_variant 0.33
clpC1 4038896 c.1809C>T synonymous_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0