TB-Profiler result

Run: ERR3132189
Summary

Run ID: ERR3132189

Sample name:

Date: 01-04-2023 00:28:06

Number of reads: 2568276

Percentage reads mapped: 99.68

Strain: lineage4.3.3;lineage4.1.4

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 0.71
lineage4.1 Euro-American T;X;H None 0.28
lineage4.1.4 Euro-American T;X;H None 0.26
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.73
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 0.71 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.71 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.73 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.75 ethambutol
gid 4407952 p.Pro84Leu missense_variant 0.73 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.72
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.66
rpoC 765150 p.Gly594Glu missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778042 p.Ala147Thr missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.69
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168298 p.Pro772Leu missense_variant 0.2
PPE35 2168998 p.Ile539Val missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.7
thyA 3073868 p.Thr202Ala missense_variant 0.66
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.71
embC 4242182 p.Ala774Ser missense_variant 0.7
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 0.66
gid 4408156 p.Leu16Arg missense_variant 0.73