TB-Profiler result

Run: ERR4423626
Summary

Run ID: ERR4423626

Sample name:

Date: 01-04-2023 05:55:47

Number of reads: 2173627

Percentage reads mapped: 92.46

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 0.99
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288766 p.Leu159Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326302 p.Trp391* stop_gained 0.94 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 8999 p.Leu566Phe missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472101 n.256G>T non_coding_transcript_exon_variant 0.18
rrl 1476130 n.2473G>T non_coding_transcript_exon_variant 0.18
inhA 1673406 c.-796C>T upstream_gene_variant 1.0
inhA 1674057 c.-145C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156133 c.-22A>G upstream_gene_variant 0.11
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.93
Rv1979c 2222149 p.Arg339His missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518194 p.Pro27Arg missense_variant 0.12
thyA 3073754 p.Glu240Lys missense_variant 0.14
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449549 p.Asn349Thr missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641901 p.Val123Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246554 p.Arg14Gln missense_variant 0.98
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4327479 c.-6G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407993 p.Ser70Arg missense_variant 1.0