TB-Profiler result

Run: ERR11050086
Summary

Run ID: ERR11050086

Sample name:

Date: 02-04-2023 10:57:21

Number of reads: 2735497

Percentage reads mapped: 99.42

Strain: lineage4

Drug-resistance: HR-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
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
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.19
fgd1 491270 p.Tyr163Cys missense_variant 1.0
mshA 576113 p.Arg256Gly missense_variant 0.25
mshA 576456 p.Val370Gly missense_variant 0.2
mshA 576606 p.Ala420Gly missense_variant 0.33
mshA 576609 p.Ala421Gly missense_variant 0.22
mshA 576613 c.1266A>C synonymous_variant 0.44
mshA 576616 c.1269G>C synonymous_variant 0.2
mshA 576618 p.His424Pro missense_variant 0.31
rpoB 761482 p.Ala559Gly missense_variant 0.21
rpoC 764367 p.Gly333Ala missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416430 c.918G>C synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474571 n.914G>A non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154915 c.1197A>G synonymous_variant 1.0
PPE35 2170041 p.Thr191Arg missense_variant 0.17
PPE35 2170069 p.Pro182Ala missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.28
pepQ 2860159 p.Ala87Gly missense_variant 0.21
Rv2752c 3064823 p.Val457Leu missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.67
fbiD 3339751 p.Ala212Pro missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>G upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.39
embB 4247016 p.Ser168Trp missense_variant 0.33
embB 4247020 c.507C>G synonymous_variant 0.15
embB 4248328 c.1815G>C synonymous_variant 0.29
whiB6 4338200 p.Asp108His missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0