TB-Profiler result

Run: ERR4814675
Summary

Run ID: ERR4814675

Sample name:

Date: 01-04-2023 13:25:43

Number of reads: 375779

Percentage reads mapped: 99.54

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154979 p.Leu378Pro missense_variant 0.25 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576488 p.Val381His missense_variant 0.4
mshA 576751 p.Lys468Asn missense_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764922 p.Glu518Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154510 c.1602G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170385 c.228G>T synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289720 c.-479C>T upstream_gene_variant 0.18
kasA 2518164 p.Thr17Ile missense_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064799 p.Arg465Trp missense_variant 0.25
thyA 3073890 c.582G>A synonymous_variant 0.2
thyA 3074654 c.-183T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3640911 c.-624C>T upstream_gene_variant 0.17
fbiB 3641584 p.Val17Asp missense_variant 0.12
fbiB 3641617 p.Asp28Gly missense_variant 0.11
fbiB 3642086 c.554delA frameshift_variant 0.29
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249502 p.Gln997Lys missense_variant 0.17
embB 4249548 p.Phe1012Ser missense_variant 0.18
aftB 4268721 p.Arg39Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0