Run ID: SRR20139560
Sample name:
Date: 03-04-2023 21:50:07
Number of reads: 2915952
Percentage reads mapped: 99.7
Strain: lineage4.8
Drug-resistance: MDR-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 |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
rpsL | 781821 | p.Lys88Gln | missense_variant | 0.77 | streptomycin |
katG | 2154611 | c.1500delG | frameshift_variant | 1.0 | isoniazid |
pncA | 2288836 | p.Asp136Asn | missense_variant | 1.0 | pyrazinamide |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol |
embB | 4249583 | p.Asp1024Asn | missense_variant | 1.0 | ethambutol |
ethA | 4326585 | c.888delG | frameshift_variant | 0.14 | ethionamide |
ethA | 4326731 | c.742dupG | frameshift_variant | 0.14 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_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 | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rpsA | 1834606 | c.1065C>T | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726121 | c.-72C>T | upstream_gene_variant | 1.0 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4326446 | p.Gly343Glu | missense_variant | 0.11 |
ethA | 4327418 | p.Ala19Glu | missense_variant | 0.34 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408103 | p.Gly34Arg | missense_variant | 0.13 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |