TB-Profiler result

Run: ERR4813302
Summary

Run ID: ERR4813302

Sample name:

Date: 01-04-2023 12:39:48

Number of reads: 556131

Percentage reads mapped: 99.64

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 761110 p.Asp435Val missense_variant 1.0 rifampicin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7704 c.407delC frameshift_variant 0.15
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760872 p.Glu356* stop_gained 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766645 c.3276A>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778150 p.Gln111* stop_gained 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475135 n.1478G>A non_coding_transcript_exon_variant 0.29
rrl 1475242 n.1585G>T non_coding_transcript_exon_variant 0.29
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168998 p.Ile539Val missense_variant 1.0
PPE35 2169900 p.Gly238Glu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289762 c.-521G>A upstream_gene_variant 0.11
kasA 2518604 p.Val164Met missense_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2518989 p.Thr292Ser missense_variant 0.14
folC 2747087 p.Ala171Glu missense_variant 0.12
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
rpoA 3877785 c.723C>T synonymous_variant 0.1
rpoA 3877795 p.Pro238Arg missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039750 p.Thr319Ala missense_variant 0.1
panD 4044203 p.Thr27Ala missense_variant 0.14
embC 4239858 c.-5G>T upstream_gene_variant 0.14
embC 4241297 p.Ala479Ser missense_variant 0.12
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267198 p.Tyr547His missense_variant 0.11
ethA 4326055 c.1419C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0