TB-Profiler result

Run: SRR13232729
Summary

Run ID: SRR13232729

Sample name:

Date: 03-04-2023 08:43:53

Number of reads: 4821313

Percentage reads mapped: 99.45

Strain: lineage4.3.3;lineage4.2.1.1

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.21
lineage4.2 Euro-American H;T;LAM None 0.78
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.81
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.21
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.78
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
rpoB 761139 p.His445Asp missense_variant 0.14 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.85 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.21 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.79 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.23 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288717 p.Met175Ile missense_variant 0.81 pyrazinamide
pncA 2289096 p.Asp49Gly missense_variant 0.12 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.18 kanamycin
alr 3841083 p.Leu113Arg missense_variant 0.24 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 0.15 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.25 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.78 ethambutol
gid 4408115 c.87delC frameshift_variant 0.74 streptomycin
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 8040 p.Gly247Ser missense_variant 0.28
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 0.19
rpoC 767123 p.Val1252Met missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.8
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.21
fbiC 1304962 p.Trp678Gly missense_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674102 c.-100C>A upstream_gene_variant 0.82
rpsA 1834836 p.Met432Thr missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.2
PPE35 2169879 p.Phe245Cys missense_variant 0.72
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.2
folC 2746340 p.Ala420Val missense_variant 0.22
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.25
ald 3086742 c.-78A>C upstream_gene_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.39
Rv3083 3449006 p.His168Pro missense_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612349 c.768A>C synonymous_variant 0.81
rpoA 3878618 c.-111A>C upstream_gene_variant 0.21
rpoA 3878637 c.-130G>C upstream_gene_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.22
ddn 3987092 p.Glu83Asp missense_variant 0.86
clpC1 4038287 c.2418C>T synonymous_variant 0.22
clpC1 4038968 c.1737G>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.24
embB 4246584 p.Arg24Pro missense_variant 0.46
ethA 4327292 p.Thr61Arg missense_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.22
gid 4408213 c.-11C>T upstream_gene_variant 0.81