TB-Profiler result

Run: ERR2516557
Summary

Run ID: ERR2516557

Sample name:

Date: 31-03-2023 21:36:12

Number of reads: 3901181

Percentage reads mapped: 99.75

Strain: lineage4.1.4

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.4 Euro-American T;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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpoB 761167 p.Pro454Arg missense_variant 0.99 rifampicin
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.89 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407845 c.357delC frameshift_variant 1.0 streptomycin
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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778042 p.Ala147Thr missense_variant 1.0
mmpR5 779005 p.Gly6Trp missense_variant 0.12
mmpR5 779420 c.436_437dupAT frameshift_variant 0.52
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473025 n.1180A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168298 p.Pro772Leu missense_variant 1.0
PPE35 2170035 p.Val193Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fbiD 3338923 c.-195T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269294 p.Met180Ile missense_variant 1.0
ethA 4327298 p.Met59Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0