TB-Profiler result

Run: SRR10809163
Summary

Run ID: SRR10809163

Sample name:

Date: 02-04-2023 19:26:30

Number of reads: 821177

Percentage reads mapped: 99.68

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 8724 p.Gln475Lys missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.28
rpoC 764088 p.Leu240His missense_variant 0.12
rpoC 765802 p.Phe811Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406219 c.1122T>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918514 p.Val192Gly missense_variant 0.16
tlyA 1918565 p.Leu209Pro missense_variant 0.12
PPE35 2169757 p.Asn286Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859675 c.743delA frameshift_variant 0.15
Rv2752c 3065728 p.Ala155Val missense_variant 1.0
ald 3087604 p.Ala262Val missense_variant 1.0
ald 3087672 c.854delA frameshift_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3642403 p.His290Leu missense_variant 0.12
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878465 p.Thr15Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0