Run ID: ERR1034680
Sample name:
Date: 31-03-2023 09:33:22
Number of reads: 5642518
Percentage reads mapped: 99.58
Strain: lineage4.3.4.1;lineage4.1.2.1
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.87 |
lineage4.1 | Euro-American | T;X;H | None | 0.12 |
lineage4.1.2 | Euro-American | T;H | None | 0.11 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.88 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.13 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 0.89 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.18 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | missense_variant | 0.84 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.17 | rifampicin |
rpoC | 764363 | p.Gly332Arg | missense_variant | 0.26 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.11 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155167 | p.Ser315Thr | missense_variant | 0.87 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.16 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.15 | ethambutol |
gid | 4407967 | p.Leu79Ser | missense_variant | 0.87 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7587 | c.286C>T | synonymous_variant | 0.19 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.14 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.16 |
rpoC | 762836 | c.-534C>G | upstream_gene_variant | 0.17 |
rpoC | 764863 | c.1494G>C | synonymous_variant | 0.17 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.85 |
rpoC | 766628 | p.Arg1087Gly | missense_variant | 0.13 |
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 |
inhA | 1674952 | p.Pro251Ala | missense_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.18 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.35 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.15 |
ahpC | 2726323 | p.Pro44Arg | missense_variant | 0.86 |
ribD | 2986729 | c.-110G>A | upstream_gene_variant | 0.92 |
Rv2752c | 3064552 | p.Arg547Pro | missense_variant | 0.2 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.84 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.83 |
rpoA | 3878647 | c.-140delG | upstream_gene_variant | 0.12 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.87 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.12 |
embC | 4242425 | p.Arg855Gly | missense_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.27 |
ubiA | 4269133 | p.Gly234Val | missense_variant | 0.89 |
ubiA | 4269296 | p.Met180Val | missense_variant | 0.14 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.15 |
ethA | 4326344 | p.Ile377Ser | missense_variant | 0.13 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.84 |