TB-Profiler result

Run: ERR257884
Summary

Run ID: ERR257884

Sample name:

Date: 31-03-2023 22:21:57

Number of reads: 555827

Percentage reads mapped: 77.62

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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.93 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
fgd1 491270 p.Tyr163Cys missense_variant 1.0
ccsA 620532 c.642T>G synonymous_variant 0.25
ccsA 620698 p.Val270Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407383 c.-44delG upstream_gene_variant 0.25
embR 1416192 p.Gly386Cys missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472266 n.421C>T non_coding_transcript_exon_variant 0.15
rrs 1472355 n.510C>A non_coding_transcript_exon_variant 0.14
rrl 1474571 n.914G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154915 c.1197A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517935 c.-180C>T upstream_gene_variant 0.14
eis 2714242 p.His364Arg missense_variant 0.15
folC 2747217 p.Glu128Lys missense_variant 0.17
Rv2752c 3065176 p.Ser339Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086948 c.129G>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642250 p.Asp239Gly missense_variant 0.17
alr 3841069 p.Ile118Val missense_variant 0.14
clpC1 4040850 c.-146G>C upstream_gene_variant 0.22
embC 4241280 c.1420delG frameshift_variant 0.12
embC 4242357 c.2497_2499dupAAC conservative_inframe_insertion 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0