Run ID: ERR1034603
Sample name:
Date: 31-03-2023 09:29:25
Number of reads: 24744955
Percentage reads mapped: 99.31
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 |
---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7570 | p.Ala90Val | missense_variant | 0.17 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7581 | p.Asp94Tyr | missense_variant | 0.68 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.95 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289224 | p.Ile6Met | missense_variant | 1.0 | pyrazinamide |
embB | 4247495 | p.Asp328Tyr | missense_variant | 1.0 | ethambutol |
ethA | 4327323 | c.150delT | 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 |
rpoB | 761460 | p.Arg552Ser | missense_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416187 | c.1161C>T | synonymous_variant | 1.0 |
embR | 1417195 | c.153A>G | synonymous_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102627 | c.406_415delCCCGGCATGA | frameshift_variant | 0.16 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.24 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.61 |
thyX | 3067959 | c.-14C>G | upstream_gene_variant | 0.13 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.26 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087388 | c.572dupG | frameshift_variant | 0.92 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474504 | c.498G>A | synonymous_variant | 1.0 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.12 |
embC | 4239763 | c.-100C>T | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4243218 | c.-15C>G | upstream_gene_variant | 1.0 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407980 | p.Pro75Ser | missense_variant | 1.0 |