TB-Profiler result

Run: SRR5341249
Summary

Run ID: SRR5341249

Sample name:

Date: 04-04-2023 10:09:58

Number of reads: 918487

Percentage reads mapped: 99.45

Strain: lineage3.1

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 9788 c.2487C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575414 c.69T>A synonymous_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763856 p.Glu163Lys missense_variant 0.12
rpoC 763998 p.Asp210Gly missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303428 c.498C>A synonymous_variant 0.93
fbiC 1304265 c.1335C>T synonymous_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473691 n.34T>A non_coding_transcript_exon_variant 0.12
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167770 p.Ser948Ile missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.63
PPE35 2170053 p.Thr187Ser missense_variant 0.68
Rv1979c 2222561 p.Ala202Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.14
kasA 2518609 p.Met165Ile missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
pepQ 2859833 p.Ala196Ser missense_variant 0.17
thyA 3073743 c.729T>C synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642005 c.471C>G synonymous_variant 1.0
fbiB 3642584 c.1050G>T synonymous_variant 0.13
clpC1 4040276 c.429C>A synonymous_variant 0.13
embC 4240706 p.Val282Met missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242688 p.Gln942His missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246859 p.Val116Ile missense_variant 0.12
ubiA 4268992 p.Asp281Val missense_variant 0.11
ethA 4326912 p.Val188Ile missense_variant 1.0
whiB6 4338364 p.Cys53Phe missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.92