TB-Profiler result

Run: SRR5341259
Summary

Run ID: SRR5341259

Sample name:

Date: 04-04-2023 10:11:51

Number of reads: 901163

Percentage reads mapped: 99.51

Strain: lineage2.2.1

Drug-resistance: Other

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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 0.88
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.91
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
folC 2747471 p.Ile43Thr missense_variant 0.12 para-aminosalicylic_acid
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 8685 p.Ile462Val missense_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.78
mshA 576751 p.Lys468Asn missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 0.89
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.95
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 0.19
Rv1258c 1406760 c.580_581insC frameshift_variant 0.86
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.91
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 2169485 c.1120_1127delGTTGGGAA frameshift_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.16
ahpC 2726338 p.Val49Gly missense_variant 0.22
ahpC 2726341 p.Val50Gly missense_variant 0.27
Rv2752c 3065315 p.Glu293* stop_gained 0.17
thyX 3067467 p.Ala160Val missense_variant 0.86
thyX 3068145 c.-200C>A upstream_gene_variant 0.91
thyA 3074641 c.-170C>T upstream_gene_variant 0.33
thyA 3074645 c.-174T>G upstream_gene_variant 0.3
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 0.78
alr 3840298 c.1122delC frameshift_variant 0.12
clpC1 4039484 c.1221T>G synonymous_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245453 p.Ala741Ser missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.9