TB-Profiler result

Run: SRR10380045
Summary

Run ID: SRR10380045

Sample name:

Date: 02-04-2023 17:25:06

Number of reads: 2619403

Percentage reads mapped: 99.61

Strain: lineage4.8;lineage4.3.4.2

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.9
lineage4.3.4 Euro-American (LAM) LAM RD174 0.09
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.05
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 0.12 isoniazid
pncA 2288815 p.Ala143Thr missense_variant 0.13 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.17 kanamycin
embB 4247431 p.Met306Ile missense_variant 0.12 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 0.24
rpoC 764840 p.Ile491Val missense_variant 0.11
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 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154696 c.1416A>G synonymous_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067954 c.-9G>A upstream_gene_variant 0.1
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.21
rpoA 3878630 c.-123G>C upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248933 p.Asn807Thr missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0