TB-Profiler result

Run: ERR4553971
Summary

Run ID: ERR4553971

Sample name:

Date: 01-04-2023 06:27:15

Number of reads: 941998

Percentage reads mapped: 99.58

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 0.98
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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288934 p.Tyr103Cys missense_variant 1.0 pyrazinamide
embB 4249583 p.Asp1024Asn missense_variant 0.89 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 9304 p.Gly668Asp missense_variant 1.0
rpoB 759939 p.Pro45Ala missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475090 n.1433A>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169740 p.Asn291Lys missense_variant 0.12
PPE35 2169743 c.870G>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 0.9
alr 3840864 p.Asp186Gly missense_variant 0.86
rpoA 3877553 p.Glu319Lys missense_variant 0.88
embC 4240390 p.Asn176Lys missense_variant 0.94
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242767 p.Arg969Gly missense_variant 0.12
embC 4242803 p.Val981Leu missense_variant 0.33
embB 4248319 c.1806A>T synonymous_variant 0.19
embB 4249408 c.2895G>A synonymous_variant 0.75
ethA 4326129 p.Gln449* stop_gained 0.93
ethA 4327161 p.Ile105Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407551 p.Met218Val missense_variant 0.92