TB-Profiler result

Run: SRR4034072
Summary

Run ID: SRR4034072

Sample name:

Date: 04-04-2023 06:33:34

Number of reads: 497832

Percentage reads mapped: 99.54

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
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
gyrA 9380 p.Met693Ile missense_variant 0.29
gyrA 9450 p.Val717Leu missense_variant 0.13
gyrA 9719 c.2418G>T synonymous_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576356 p.Ala337Ser missense_variant 0.22
ccsA 620402 p.Trp171Leu missense_variant 0.18
ccsA 620409 c.519C>A synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760446 p.Asp214Asn missense_variant 0.12
rpoB 762243 p.Arg813Trp missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764720 p.Leu451Met missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775912 c.2569C>A synonymous_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
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 1305383 p.Arg818Leu missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407371 c.-31C>G upstream_gene_variant 0.15
embR 1416673 c.675G>T synonymous_variant 0.18
embR 1416689 p.Arg220Gln missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472074 n.229G>A non_coding_transcript_exon_variant 0.17
rrs 1472501 n.656G>T non_coding_transcript_exon_variant 0.18
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.2
rrl 1474570 n.913G>T non_coding_transcript_exon_variant 0.17
rrl 1475145 n.1488C>T non_coding_transcript_exon_variant 0.29
rrl 1475188 n.1531C>A non_coding_transcript_exon_variant 0.25
rrl 1475218 n.1561C>A non_coding_transcript_exon_variant 0.12
rrl 1475740 n.2083G>T non_coding_transcript_exon_variant 0.18
rrl 1475972 n.2315C>A non_coding_transcript_exon_variant 0.22
rrl 1476772 n.3115C>A non_coding_transcript_exon_variant 0.14
fabG1 1673767 p.Asn110Asp missense_variant 0.14
rpsA 1833851 p.Lys104Glu missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834475 p.Arg312Ser missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102258 p.Ser262Tyr missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168456 c.2157C>A synonymous_variant 0.18
PPE35 2169119 c.1494G>T synonymous_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.47
PPE35 2169684 p.Gly310Asp missense_variant 0.17
PPE35 2169919 p.Leu232Ile missense_variant 0.22
PPE35 2170217 c.396G>T synonymous_variant 0.12
Rv1979c 2221903 p.Ala421Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289447 c.-206G>C upstream_gene_variant 0.33
pncA 2290103 c.-862C>T upstream_gene_variant 0.14
kasA 2518309 p.Lys65Asn missense_variant 0.17
kasA 2518324 p.Ser70Arg missense_variant 0.18
ahpC 2726338 p.Val49Gly missense_variant 0.29
Rv2752c 3065048 p.Leu382Met missense_variant 0.29
Rv2752c 3066012 c.180C>A synonymous_variant 0.14
Rv2752c 3066039 c.153C>A synonymous_variant 0.15
Rv2752c 3066302 c.-111C>A upstream_gene_variant 0.17
Rv2752c 3067007 c.-816C>A upstream_gene_variant 0.18
thyX 3067291 p.Leu219Phe missense_variant 0.22
thyX 3067525 p.Ala141Ser missense_variant 0.29
thyA 3073933 p.Ser180Ile missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474027 c.21C>A synonymous_variant 0.15
fprA 3474316 p.Val104Ile missense_variant 0.33
fprA 3474390 p.Phe128Leu missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640810 p.Gln90* stop_gained 0.13
alr 3840985 p.Arg146Cys missense_variant 0.15
embC 4239960 p.Ala33Asp missense_variant 0.25
embC 4240132 c.270C>A synonymous_variant 0.22
embC 4240146 p.Ala95Val missense_variant 0.22
embC 4240792 p.Met310Ile missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244072 c.840C>T synonymous_variant 0.17
embA 4244986 p.Gly585Asp missense_variant 0.18
embA 4246204 p.Arg991Leu missense_variant 0.22
embB 4248327 p.Ala605Gly missense_variant 0.12
aftB 4267042 p.Arg599Ser missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267787 c.1050G>T synonymous_variant 0.4
ethA 4327671 c.-198C>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0