TB-Profiler result

Run: ERR10748295
Summary

Run ID: ERR10748295

Sample name:

Date: 31-03-2023 10:50:13

Number of reads: 1290967

Percentage reads mapped: 99.72

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H 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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethR 4327876 p.Phe110Leu missense_variant 1.0 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 491356 p.Phe192Val missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 0.97
mshA 575980 p.Asp211Glu missense_variant 1.0
mshA 576448 c.1101A>C synonymous_variant 0.2
mshA 576468 p.Val374Gly missense_variant 0.38
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.97
PPE35 2168171 c.2442C>A synonymous_variant 0.18
PPE35 2168303 c.2310G>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289220 p.Asp8His missense_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.33
whiB7 3568428 c.252A>G synonymous_variant 0.22
alr 3840263 c.1158C>T synonymous_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
embC 4240495 c.633T>G synonymous_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.22
aftB 4267091 c.1746C>A synonymous_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0