Run ID: ERR4796896
Sample name:
Date: 01-04-2023 07:11:20
Number of reads: 2533633
Percentage reads mapped: 99.61
Strain: lineage4.8
Drug-resistance: XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rplC | 801268 | p.Cys154Arg | missense_variant | 1.0 | linezolid |
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 | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide |
ald | 3087252 | c.436_437dupGC | frameshift_variant | 1.0 | cycloserine |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol |
ethA | 4326889 | c.584dupC | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.18 |
rpoB | 761461 | p.Arg552His | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpR5 | 779243 | p.Val85Gly | missense_variant | 0.63 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475952 | n.2295A>C | non_coding_transcript_exon_variant | 0.19 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.25 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.15 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.5 |
rpoA | 3878658 | c.-151A>C | upstream_gene_variant | 0.2 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.35 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.33 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.99 |
Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 |