Run ID: ERR2516687
Sample name:
Date: 31-03-2023 21:40:52
Number of reads: 3462190
Percentage reads mapped: 99.81
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 | 1.0 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.62 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
pncA | 2289061 | p.Thr61Pro | missense_variant | 0.11 | pyrazinamide |
pncA | 2289252 | c.-11A>C | upstream_gene_variant | 0.69 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7615 | p.Leu105Arg | missense_variant | 0.22 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 761998 | p.Leu731Pro | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
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 | 1474943 | n.1286A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1475019 | n.1362T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475940 | n.2283C>T | non_coding_transcript_exon_variant | 0.13 |
rpsA | 1834234 | c.693G>A | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 |
katG | 2154974 | p.Thr380Pro | missense_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.26 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289162 | p.Leu27Arg | missense_variant | 0.22 |
folC | 2747481 | p.Glu40Lys | missense_variant | 1.0 |
Rv2752c | 3065293 | p.Val300Ala | missense_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.23 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
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 | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.29 |
embC | 4239763 | c.-100C>T | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4247884 | c.1371C>A | synonymous_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408061 | p.His48Tyr | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |