Run ID: ERR459444
Sample name:
Date: 01-04-2023 06:28:15
Number of reads: 1769000
Percentage reads mapped: 99.43
Strain: lineage4.8
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 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6579 | p.Ser447Phe | missense_variant | 0.75 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrB | 6738 | p.Thr500Asn | missense_variant | 0.35 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2156093 | c.18dupA | frameshift_variant | 0.95 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
mshA | 576057 | c.712dupG | frameshift_variant | 0.2 |
mshA | 576372 | p.Ala342Glu | missense_variant | 0.72 |
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 | 1476456 | n.2801delT | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476704 | n.3053delC | non_coding_transcript_exon_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2156151 | c.-40T>C | upstream_gene_variant | 0.69 |
PPE35 | 2170530 | p.Ala28Glu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726568 | p.Asn126Asp | missense_variant | 1.0 |
thyA | 3074422 | p.Pro17Leu | missense_variant | 1.0 |
embC | 4239809 | c.-54C>T | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |