TB-Profiler result

Run: ERR10748237
Summary

Run ID: ERR10748237

Sample name:

Date: 31-03-2023 10:48:22

Number of reads: 442423

Percentage reads mapped: 99.78

Strain: lineage4.3.2.1

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
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 761140 p.His445Leu missense_variant 1.0 rifampicin
mmpR5 779191 p.Ser68Gly missense_variant 0.11 clofazimine, bedaquiline
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155500 p.Trp204* stop_gained 1.0 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 0.97 isoniazid
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620025 c.135G>T synonymous_variant 0.12
rpoB 760962 p.Gly386Cys missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765411 p.Tyr681Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776401 c.2079delC frameshift_variant 0.1
mmpL5 777426 p.Thr352Ser missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781520 c.-40C>T upstream_gene_variant 0.14
atpE 1460920 c.-125T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475630 n.1973A>T non_coding_transcript_exon_variant 0.18
rrl 1475923 n.2266T>A non_coding_transcript_exon_variant 0.1
rrl 1476663 n.3006C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103061 c.-19C>A upstream_gene_variant 0.11
Rv1979c 2222653 p.Ala171Glu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987123 c.285C>T synonymous_variant 0.11
Rv2752c 3064916 p.Gly426Ser missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449825 p.Ser441Phe missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840598 p.Met275Val missense_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038652 p.Gly685Ser missense_variant 0.13
clpC1 4038696 p.Thr670Ile missense_variant 0.11
clpC1 4040471 c.234T>A synonymous_variant 0.12
embC 4241785 c.1924delT frameshift_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246325 c.-189G>A upstream_gene_variant 1.0
ubiA 4269022 p.Ala271Val missense_variant 0.11
ethA 4326566 p.Arg303Leu missense_variant 0.1
ethR 4327873 p.Val109Met missense_variant 0.14
whiB6 4338177 c.345G>A synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0