Run ID: ERR1873448
Sample name:
Date: 14-08-2022 13:32:44
Number of reads: 6152263
Percentage reads mapped: 96.13
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 |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.2 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrs | 1473247 | n.1402C>T | non_coding_transcript_exon_variant | 0.41 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288827 | p.Val139Met | missense_variant | 1.0 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326876 | c.597delC | frameshift_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6608 | p.Val457Leu | missense_variant | 1.0 |
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 | 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 |
rplC | 801354 | c.546G>A | synonymous_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.18 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.33 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449616 | p.Met371Ile | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3878641 | c.-135delG | upstream_gene_variant | 0.1 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.27 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ubiA | 4269296 | p.Met180Val | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |