Run ID: SRR14801551
Sample name:
Date: 03-04-2023 11:52:18
Number of reads: 1306740
Percentage reads mapped: 99.45
Strain: lineage4.2.1
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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288775 | p.Leu156Pro | missense_variant | 0.89 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.97 | kanamycin |
embB | 4247402 | p.Ser297Ala | missense_variant | 0.95 | ethambutol |
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 |
fgd1 | 491247 | c.465C>T | synonymous_variant | 1.0 |
mshA | 576113 | p.Arg256Gly | missense_variant | 0.25 |
ccsA | 619969 | p.Val27Ile | missense_variant | 1.0 |
rpoB | 763151 | p.Phe1115Leu | missense_variant | 0.22 |
rpoC | 764367 | p.Gly333Ala | missense_variant | 0.16 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
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 |
fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.29 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102817 | p.Leu76Val | missense_variant | 0.1 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.94 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.18 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519071 | p.Asp319Glu | missense_variant | 0.16 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.25 |
Rv2752c | 3064823 | p.Val457Leu | missense_variant | 0.16 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.98 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.5 |
fbiD | 3339746 | p.Ala210Gly | missense_variant | 0.57 |
fbiD | 3339749 | p.Val211Gly | missense_variant | 0.36 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.98 |
whiB7 | 3568428 | c.252A>G | synonymous_variant | 0.75 |
whiB7 | 3568431 | c.249C>G | synonymous_variant | 0.3 |
rpoA | 3878590 | c.-83G>C | upstream_gene_variant | 0.4 |
rpoA | 3878597 | c.-90G>C | upstream_gene_variant | 0.4 |
rpoA | 3878637 | c.-130G>C | upstream_gene_variant | 0.5 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.33 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.33 |
embC | 4240413 | p.Leu184Arg | missense_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243225 | c.-8C>T | upstream_gene_variant | 1.0 |
embA | 4245835 | p.Leu868Arg | missense_variant | 0.17 |
embB | 4246529 | p.Ser6Arg | missense_variant | 0.33 |
embB | 4247033 | p.Ser174Arg | missense_variant | 0.21 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.21 |
embB | 4249594 | c.3081G>A | synonymous_variant | 1.0 |
ethA | 4326632 | p.His281Pro | missense_variant | 1.0 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 1.0 |
whiB6 | 4338473 | c.49A>C | synonymous_variant | 0.83 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |