Run ID: ERR11082095
Sample name:
Date: 10-04-2023 00:12:40
Number of reads: 4014731
Percentage reads mapped: 99.67
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 | 6742 | p.Glu501Asp | missense_variant | 0.96 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.86 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155699 | p.Asn138Ser | missense_variant | 1.0 | isoniazid |
pncA | 2289046 | p.Ser66Pro | missense_variant | 1.0 | pyrazinamide |
ethA | 4326696 | c.777dupC | frameshift_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5392 | c.153C>T | synonymous_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.2 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471658 | n.-187delC | upstream_gene_variant | 1.0 |
rrs | 1471868 | n.23T>G | non_coding_transcript_exon_variant | 0.99 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2103178 | c.-136G>A | upstream_gene_variant | 1.0 |
PPE35 | 2168076 | p.Thr846Met | missense_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2987597 | c.759C>T | synonymous_variant | 1.0 |
Rv2752c | 3064883 | p.Ser437Gly | missense_variant | 1.0 |
thyA | 3073746 | c.726C>T | synonymous_variant | 1.0 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4247862 | p.Ile450Ser | missense_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 |