TB-Profiler result

Run: ERR4812768

Summary

Run ID: ERR4812768

Sample name:

Date: 01-04-2023 12:19:17

Number of reads: 549450

Percentage reads mapped: 99.21

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 0.98
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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpoB 761115 p.Asn437Asp missense_variant 1.0 rifampicin
tlyA 1918634 p.Gly232Asp missense_variant 0.94 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 1.0 ethambutol
gid 4407952 p.Pro84Leu missense_variant 1.0 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
gyrB 5460 p.Gly74Asp missense_variant 0.12
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
ccsA 620376 c.486G>A synonymous_variant 0.15
rpoB 761257 p.Glu484Gly missense_variant 0.22
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
atpE 1461065 c.21C>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473448 n.-210G>T upstream_gene_variant 0.2
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154111 c.2001C>G synonymous_variant 0.17
PPE35 2168998 p.Ile539Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714963 c.369delC frameshift_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613040 p.Arg26Gln missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240507 c.645G>A synonymous_variant 0.22
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245133 p.Trp634Leu missense_variant 0.15
embB 4247818 c.1305C>T synonymous_variant 0.25
ethA 4327467 p.Glu3* stop_gained 0.12
ethR 4327786 p.Val80Phe missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0