Run ID: ERR10748150
Sample name:
Date: 31-03-2023 10:45:46
Number of reads: 466591
Percentage reads mapped: 99.84
Strain: lineage4.1.1.3
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 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | 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 |
katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288827 | p.Val139Met | missense_variant | 1.0 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326876 | c.597delC | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5070 | c.-170C>T | upstream_gene_variant | 0.2 |
gyrB | 6115 | p.Gln292His | missense_variant | 0.25 |
gyrB | 6608 | p.Val457Leu | missense_variant | 1.0 |
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 | 490657 | c.-126T>C | upstream_gene_variant | 0.12 |
fgd1 | 490967 | p.Gly62Asp | missense_variant | 0.12 |
ccsA | 620187 | c.297C>A | synonymous_variant | 0.11 |
rpoB | 763110 | p.Lys1102* | stop_gained | 0.29 |
rpoB | 763147 | p.Ser1114Leu | missense_variant | 0.25 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 778285 | p.Pro66Ser | missense_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801354 | c.546G>A | synonymous_variant | 1.0 |
fbiC | 1303404 | c.474A>G | synonymous_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1674321 | c.120G>T | synonymous_variant | 0.29 |
rpsA | 1834583 | p.Val348Leu | missense_variant | 0.11 |
rpsA | 1834856 | p.Glu439* | stop_gained | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102258 | p.Ser262Cys | missense_variant | 0.11 |
katG | 2154087 | c.2025C>T | synonymous_variant | 0.12 |
katG | 2154308 | p.Asn602His | missense_variant | 0.13 |
katG | 2155469 | p.Asp215Tyr | missense_variant | 0.18 |
katG | 2156266 | c.-155G>A | upstream_gene_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2859596 | p.Ala275Thr | missense_variant | 0.11 |
pepQ | 2860223 | p.Ser66Pro | missense_variant | 1.0 |
ald | 3086713 | c.-107C>A | upstream_gene_variant | 0.11 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449616 | p.Met371Ile | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3840353 | c.1068T>C | synonymous_variant | 0.12 |
rpoA | 3877692 | c.816G>A | synonymous_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.96 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ethA | 4328245 | c.-772C>A | upstream_gene_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |