Run ID: ERR1034784
Sample name:
Date: 31-03-2023 09:40:50
Number of reads: 20240151
Percentage reads mapped: 99.78
Strain: lineage4.3.4.2
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 | 0.99 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.99 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.92 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289052 | p.Tyr64Asp | missense_variant | 0.99 | pyrazinamide |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.99 | ethambutol |
ethA | 4326716 | c.757delT | frameshift_variant | 0.99 | ethionamide, 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 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.99 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.99 |
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 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2155017 | c.1095G>A | synonymous_variant | 0.99 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.2 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
folC | 2747453 | p.Arg49Gln | missense_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.13 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
alr | 3840232 | p.Arg397Gly | missense_variant | 0.11 |
alr | 3841354 | p.Leu23Met | missense_variant | 0.92 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.13 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.24 |
embA | 4243190 | c.-43G>C | upstream_gene_variant | 1.0 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338600 | c.-79T>C | upstream_gene_variant | 0.99 |
gid | 4408054 | p.Leu50Arg | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |