TB-Profiler result

Run: SRR10525359
Summary

Run ID: SRR10525359

Sample name:

Date: 02-04-2023 18:33:10

Number of reads: 5401973

Percentage reads mapped: 99.52

Strain: lineage4.8

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
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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288806 p.Ala146Thr missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
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
mshA 576108 p.Ala254Gly missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
fbiB 3640974 c.-561T>G upstream_gene_variant 0.99
rpoA 3878613 c.-106A>C upstream_gene_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
embC 4241699 p.Met613Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4246567 c.54G>T synonymous_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.34
whiB6 4338234 c.288A>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0