TB-Profiler result

Run: SRR6356993
Summary

Run ID: SRR6356993

Sample name:

Date: 04-04-2023 13:40:26

Number of reads: 2321262

Percentage reads mapped: 99.53

Strain: lineage4.2.1;lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.46
lineage4.2 Euro-American H;T;LAM None 0.51
lineage4.1.2 Euro-American T;H None 0.47
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.5
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.47
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 6738 p.Thr500Asn missense_variant 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760663 p.Ala286Val missense_variant 0.48 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.58 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.47 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.89 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.41 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid
katG 2156089 c.22dupA frameshift_variant 0.46 isoniazid, isoniazid
pncA 2288806 p.Ala146Thr missense_variant 0.56 pyrazinamide
embB 4247729 p.Gly406Cys missense_variant 0.49 ethambutol
ethA 4326211 c.1261_1262dupCG frameshift_variant 0.16 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.37
fgd1 491591 p.Lys270Met missense_variant 0.47
mshA 575679 p.Asn111Ser missense_variant 0.44
mshA 576108 p.Ala254Gly missense_variant 0.32
ccsA 619969 p.Val27Ile missense_variant 0.48
rpoB 760106 c.300G>A synonymous_variant 0.4
rpoB 760115 c.309C>T synonymous_variant 0.39
rpoC 765150 p.Gly594Glu missense_variant 0.6
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406584 p.Asp253Tyr missense_variant 0.46
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156484 c.-373A>C upstream_gene_variant 0.36
katG 2156565 c.-455dupA upstream_gene_variant 0.12
PPE35 2169879 p.Phe245Cys missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.42
eis 2715340 c.-8C>T upstream_gene_variant 0.4
ribD 2986827 c.-12G>A upstream_gene_variant 0.43
ald 3086742 c.-78A>C upstream_gene_variant 0.53
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.48
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4248319 c.1806A>T synonymous_variant 0.19
embB 4249594 c.3081G>A synonymous_variant 0.38
aftB 4267274 c.1563G>A synonymous_variant 0.36
ubiA 4269148 p.Val229Ala missense_variant 0.2
ubiA 4269731 p.Ala35Thr missense_variant 0.34
ethA 4328376 c.-903G>C upstream_gene_variant 0.55
whiB6 4338513 c.9C>T synonymous_variant 0.51
whiB6 4338595 c.-75delG upstream_gene_variant 1.0