TB-Profiler result

Run: SRR6485022
Summary

Run ID: SRR6485022

Sample name:

Date: 04-04-2023 15:03:27

Number of reads: 4377592

Percentage reads mapped: 98.35

Strain: lineage4.2.1.1

Drug-resistance: Pre-XDR-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
lineage4.2.1.1 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
gyrB 6579 p.Ser447Phe missense_variant 0.5 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7566 p.Asp89Asn missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761128 p.Ser441Leu missense_variant 0.95 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.99 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoB 761828 p.His674Gln missense_variant 0.96
rpoC 764338 c.969G>A synonymous_variant 0.12
rpoC 764353 c.984G>C synonymous_variant 0.12
rpoC 766963 c.3594T>C synonymous_variant 0.12
rpoC 766972 c.3603G>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.12
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
rpsA 1833847 c.306C>G synonymous_variant 0.11
rpsA 1833856 c.315A>G synonymous_variant 0.11
rpsA 1833874 c.333T>C synonymous_variant 0.11
rpsA 1833886 c.345C>G synonymous_variant 0.11
rpsA 1833928 c.387G>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067718 c.228C>G synonymous_variant 0.12
thyX 3067721 c.225T>C synonymous_variant 0.12
thyA 3073989 c.483T>C synonymous_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.3
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4246584 p.Arg24Pro missense_variant 0.21
ethA 4326455 p.Thr340Asn missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407991 p.Gly71Glu missense_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0