TB-Profiler result

Run: ERR5864958
Summary

Run ID: ERR5864958

Sample name:

Date: 01-04-2023 23:42:13

Number of reads: 1205878

Percentage reads mapped: 98.65

Strain: lineage2.2.1

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
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8954 p.Gln551His missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9690 c.2390delA frameshift_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575688 c.345delG frameshift_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760462 p.Arg219Leu missense_variant 0.12
rpoB 760716 p.Arg304Cys missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764113 p.Tyr248* stop_gained 0.11
rpoC 764833 p.Glu488Asp missense_variant 0.8
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766740 p.Val1124Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775951 c.2530C>T synonymous_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304461 p.Asp511Asn missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407501 c.-161C>T upstream_gene_variant 0.17
embR 1417158 p.Pro64Thr missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473350 n.1505T>C non_coding_transcript_exon_variant 0.18
rrs 1473354 n.1509G>T non_coding_transcript_exon_variant 0.2
rrs 1473355 n.1510G>T non_coding_transcript_exon_variant 0.2
rrs 1473356 n.1511A>C non_coding_transcript_exon_variant 0.2
rrs 1473357 n.1512A>C non_coding_transcript_exon_variant 0.2
rrs 1473361 n.1516G>A non_coding_transcript_exon_variant 0.2
rrl 1474161 n.506_507delCC non_coding_transcript_exon_variant 0.17
rrl 1475059 n.1402G>A non_coding_transcript_exon_variant 0.4
rrl 1475060 n.1404delC non_coding_transcript_exon_variant 0.4
rrl 1475065 n.1408G>A non_coding_transcript_exon_variant 0.4
rrl 1475067 n.1410A>G non_coding_transcript_exon_variant 0.4
rrl 1475068 n.1411A>G non_coding_transcript_exon_variant 0.33
rrl 1475076 n.1419C>A non_coding_transcript_exon_variant 0.29
rrl 1475078 n.1421T>C non_coding_transcript_exon_variant 0.29
rrl 1475079 n.1422T>C non_coding_transcript_exon_variant 0.29
rrl 1475081 n.1424C>T non_coding_transcript_exon_variant 0.29
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.29
rrl 1475090 n.1433A>T non_coding_transcript_exon_variant 0.29
rrl 1475094 n.1437C>T non_coding_transcript_exon_variant 0.29
rrl 1475104 n.1447T>A non_coding_transcript_exon_variant 0.29
rrl 1475108 n.1451C>T non_coding_transcript_exon_variant 0.25
rrl 1475111 n.1454G>A non_coding_transcript_exon_variant 0.25
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.25
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.25
rrl 1475119 n.1462C>T non_coding_transcript_exon_variant 0.25
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.25
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.25
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.1
Rv1979c 2222287 p.Ala293Glu missense_variant 0.2
Rv1979c 2222372 p.Ala265Pro missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518081 c.-34C>A upstream_gene_variant 0.13
kasA 2518236 p.Ser41Ile missense_variant 0.1
Rv2752c 3067141 c.-950A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087448 p.Glu210Gly missense_variant 0.12
fbiD 3339414 c.297C>T synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474142 c.141delG frameshift_variant 0.14
fprA 3475185 c.1179C>A synonymous_variant 0.11
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642230 c.696G>T synonymous_variant 0.13
fbiB 3642535 p.Arg334Gln missense_variant 0.13
fbiB 3642705 p.Arg391Cys missense_variant 0.13
embC 4239878 c.20delC frameshift_variant 0.11
embC 4240844 p.Tyr328His missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244522 c.1290C>A synonymous_variant 0.12
embA 4244650 p.Asp473Gly missense_variant 0.12
embB 4249288 c.2778delC frameshift_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268045 c.792C>T synonymous_variant 0.12
aftB 4268265 p.Leu191Pro missense_variant 0.12
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