TB-Profiler result

Run: ERR4972590
Summary

Run ID: ERR4972590

Sample name:

Date: 01-04-2023 21:48:07

Number of reads: 127925

Percentage reads mapped: 6.1

Strain: lineage4

Drug-resistance: Pre-XDR-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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
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 7611 p.Ser104Pro missense_variant 0.4
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760007 c.201C>T synonymous_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761632 p.Ala609Glu missense_variant 0.33
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777793 p.Ala230Thr missense_variant 1.0
mmpL5 777812 p.Tyr223* stop_gained 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303458 c.528G>A synonymous_variant 0.29
fbiC 1303802 p.Ile291Asn missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474573 n.916C>T non_coding_transcript_exon_variant 0.4
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.4
ndh 2102185 c.857dupG frameshift_variant 1.0
katG 2154224 p.Gly630Cys missense_variant 0.29
PPE35 2169751 p.Gly288* stop_gained 1.0
Rv1979c 2222777 p.Ala130Thr missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517984 c.-131G>T upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2859525 c.894T>A synonymous_variant 0.4
pepQ 2860184 c.229_234delCGCGCG conservative_inframe_deletion 0.2
pepQ 2860200 c.219G>A synonymous_variant 0.22
pepQ 2860201 c.216_217delAG frameshift_variant 0.29
pepQ 2860207 c.211_212insGCGCGC conservative_inframe_insertion 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087721 p.Met301Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475061 p.Pro352His missense_variant 0.5
clpC1 4040590 p.His39Asp missense_variant 0.4
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245386 c.2154C>T synonymous_variant 0.15
embB 4247024 p.Pro171Ala missense_variant 0.67
embB 4247915 p.Arg468Ser missense_variant 0.22
embB 4249209 p.Val899Ala missense_variant 0.18
ethA 4326119 p.Arg452Pro missense_variant 1.0
whiB6 4338579 c.-58C>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0