TB-Profiler result

Run: SRR6511602
Summary

Run ID: SRR6511602

Sample name:

Date: 04-04-2023 15:14:38

Number of reads: 427874

Percentage reads mapped: 99.74

Strain: lineage4.3.4.2

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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
rpoB 761155 p.Ser450Leu missense_variant 0.66 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_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
gyrA 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761901 p.Gly699Ser missense_variant 0.17
rpoB 762324 p.Lys840Glu missense_variant 0.15
rpoC 763753 c.384C>T synonymous_variant 0.2
rpoC 764915 p.Leu516Val missense_variant 0.43
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.88
katG 2155025 p.Thr363Ser missense_variant 0.14
katG 2156521 c.-410C>T upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289527 c.-286C>A upstream_gene_variant 0.2
pncA 2289582 c.-341C>T upstream_gene_variant 0.2
eis 2714709 c.624C>T synonymous_variant 0.12
Rv2752c 3067132 c.-941T>C upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339422 p.Val102Ala missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475212 c.1206T>C synonymous_variant 0.17
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840579 p.Val281Ala missense_variant 0.12
rpoA 3878065 p.Pro148Gln missense_variant 0.14
rpoA 3878151 p.His119Gln missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242577 c.-656A>G upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244275 p.Gly348Glu missense_variant 0.14
embB 4247061 p.Pro183Gln missense_variant 0.17
embB 4247555 c.1042C>T synonymous_variant 0.12
ethR 4327703 p.Lys52Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0