Run ID: ERR2653172
Sample name:
Date: 31-03-2023 22:37:44
Number of reads: 5700797
Percentage reads mapped: 96.29
Strain: lineage4.3.3
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.99 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6735 | p.Asn499Thr | missense_variant | 0.95 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.9 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.94 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289095 | p.Asp49Glu | missense_variant | 0.99 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.99 | ethambutol |
ethA | 4327081 | p.Cys131* | stop_gained | 0.9 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5723 | p.Ala162Ser | missense_variant | 0.99 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 575240 | c.-108G>A | upstream_gene_variant | 0.97 |
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 |
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474428 | n.771C>T | non_coding_transcript_exon_variant | 0.11 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.14 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289272 | c.-31C>A | upstream_gene_variant | 0.19 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086865 | c.47dupT | frameshift_variant | 0.91 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.97 |
embC | 4242182 | p.Ala774Ser | missense_variant | 0.98 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.98 |