TB-Profiler result

Run: ERR5865004
Summary

Run ID: ERR5865004

Sample name:

Date: 01-04-2023 23:44:03

Number of reads: 1312919

Percentage reads mapped: 97.61

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 761139 p.His445Cys missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155433 c.678delG frameshift_variant 0.1 isoniazid
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_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 6689 p.Lys484Glu missense_variant 0.1
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
rpoB 760779 p.Ser325Thr missense_variant 0.17
rpoB 760912 p.Asn369Ser missense_variant 0.12
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475134 n.1477G>T non_coding_transcript_exon_variant 0.12
fabG1 1673395 c.-45C>A upstream_gene_variant 0.1
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289763 c.-523delT upstream_gene_variant 0.11
pncA 2289800 c.-559C>T upstream_gene_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448467 c.-37T>A upstream_gene_variant 0.13
Rv3083 3448768 p.Ala89Ser missense_variant 0.15
Rv3083 3449373 p.Tyr290* stop_gained 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568730 c.-51G>C upstream_gene_variant 1.0
Rv3236c 3612361 c.756C>A synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4039113 p.Ala531Asp missense_variant 0.11
clpC1 4039654 p.Thr351Ser missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326449 p.Thr342Met missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0