TB-Profiler result

Run: SRR10303294
Summary

Run ID: SRR10303294

Sample name:

Date: 02-04-2023 16:41:19

Number of reads: 2182146

Percentage reads mapped: 99.68

Strain: lineage4.3.3

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 0.96
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.97
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
pncA 2289162 p.Leu27Pro missense_variant 0.95 pyrazinamide
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 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576614 p.Arg423Gly missense_variant 0.23
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ser missense_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
rpsA 1834836 p.Met432Thr missense_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155748 p.Ala122Thr missense_variant 0.95
katG 2156196 c.-85C>T upstream_gene_variant 0.97
PPE35 2170065 p.Ala183Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.98
ahpC 2726121 c.-72C>T upstream_gene_variant 0.96
folC 2746340 p.Ala420Val missense_variant 0.99
pepQ 2860159 p.Ala87Gly missense_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.41
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 0.98
clpC1 4038968 c.1737G>A synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.2
ethA 4326125 p.Gly450Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0