TB-Profiler result

Run: ERR4813320

Summary

Run ID: ERR4813320

Sample name:

Date: 01-04-2023 12:40:26

Number of reads: 3067054

Percentage reads mapped: 99.49

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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 1.0 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575268 c.-80C>A upstream_gene_variant 0.25
mshA 575407 c.60C>T synonymous_variant 1.0
ccsA 619863 c.-28C>T upstream_gene_variant 0.5
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766079 p.Arg904Cys missense_variant 0.12
rpoC 766487 p.Pro1040Ala missense_variant 1.0
rpoC 766977 p.Gly1203Val missense_variant 0.18
rpoC 766984 c.3615G>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801216 c.408C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834683 p.Ala381Val missense_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918110 c.171C>T synonymous_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474889 p.Val295Ile missense_variant 0.13
fbiB 3642143 p.Asp203Glu missense_variant 0.22
fbiB 3642342 p.Pro270Thr missense_variant 1.0
fbiB 3642374 c.840C>A synonymous_variant 0.33
fbiB 3642701 c.1167C>A synonymous_variant 0.2
rpoA 3878565 c.-58G>C upstream_gene_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241097 p.Ser412Leu missense_variant 0.12
embC 4241109 p.Ala416Glu missense_variant 0.13
embC 4242182 p.Ala774Ser missense_variant 1.0
embC 4242654 p.Ala931Val missense_variant 1.0
embC 4242719 p.Ala953Ser missense_variant 0.15
embA 4243673 c.441C>A synonymous_variant 0.17
embB 4248631 c.2118G>T synonymous_variant 0.17
ethR 4328023 p.Arg159* stop_gained 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0