TB-Profiler result

Run: SRR6785234
Summary

Run ID: SRR6785234

Sample name:

Date: 04-04-2023 15:38:04

Number of reads: 1693505

Percentage reads mapped: 99.72

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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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
gyrB 5996 p.Tyr253Asn missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 763343 c.-27T>A upstream_gene_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304301 c.1371C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473931 n.274A>T non_coding_transcript_exon_variant 0.4
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064544 p.Met550Leu missense_variant 0.13
Rv2752c 3064600 p.Gln531Pro missense_variant 0.17
Rv2752c 3065731 p.Leu154Trp missense_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4241829 p.Lys656Met missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4249313 p.Phe934Val missense_variant 0.15
aftB 4267599 p.Phe413Ser missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408182 c.21G>T synonymous_variant 0.2
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0