TB-Profiler result

Run: SRR6485052
Summary

Run ID: SRR6485052

Sample name:

Date: 04-04-2023 15:03:48

Number of reads: 1148585

Percentage reads mapped: 99.52

Strain: lineage4.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 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 0.62 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 8922 p.Gly541Cys missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406810 c.531C>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471952 n.107G>T non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.22
fabG1 1673359 c.-81T>C upstream_gene_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
rpsA 1834158 p.Leu206* stop_gained 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714347 p.Phe329Tyr missense_variant 0.2
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449219 p.Val239Gly missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612184 p.Phe311Leu missense_variant 0.12
embC 4242032 p.Thr724Pro missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243146 c.3284A>T stop_lost&splice_region_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4249594 c.3081G>A synonymous_variant 1.0
ubiA 4269043 p.Val264Gly missense_variant 0.2
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0