Run ID: SRR18715071
Sample name:
Date: 03-04-2023 20:17:34
Number of reads: 2674479
Percentage reads mapped: 98.8
Strain: lineage4.2.1.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.2 | Euro-American | H;T;LAM | None | 1.0 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 1.0 |
lineage4.2.1.1 | Euro-American (TUR) | H3;H4 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288826 | p.Val139Ala | missense_variant | 1.0 | pyrazinamide |
embB | 4247729 | p.Gly406Ser | missense_variant | 1.0 | ethambutol |
ethA | 4326081 | c.1392dupC | frameshift_variant | 1.0 | ethionamide |
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 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.18 |
mshA | 576113 | p.Arg256Gly | missense_variant | 0.33 |
mshA | 576456 | p.Val370Gly | missense_variant | 0.23 |
mshA | 576613 | c.1266A>C | synonymous_variant | 0.33 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.14 |
mshA | 576618 | p.His424Pro | missense_variant | 0.13 |
rpoC | 764367 | p.Gly333Ala | missense_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776802 | p.Met560Thr | missense_variant | 1.0 |
mmpL5 | 777451 | p.Val344Leu | missense_variant | 1.0 |
mmpL5 | 777883 | p.Gly200Arg | missense_variant | 0.19 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.23 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.16 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519071 | p.Asp319Glu | missense_variant | 0.22 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.17 |
Rv2752c | 3065958 | c.234G>A | synonymous_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087816 | p.Cys333Gly | missense_variant | 0.12 |
fbiD | 3339751 | p.Ala212Pro | missense_variant | 0.22 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.4 |
rpoA | 3878597 | c.-90G>C | upstream_gene_variant | 0.25 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.79 |
ddn | 3987092 | p.Glu83Asp | missense_variant | 1.0 |
clpC1 | 4040786 | c.-82G>A | upstream_gene_variant | 1.0 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.16 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243190 | c.-43G>C | upstream_gene_variant | 1.0 |
embB | 4246527 | p.Ala5Gly | missense_variant | 0.44 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.27 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408213 | c.-11C>T | upstream_gene_variant | 1.0 |