Run ID: SRR23086729
Sample name:
Date: 04-04-2023 04:22:07
Number of reads: 1990820
Percentage reads mapped: 99.74
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 |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Tyr | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764363 | p.Gly332Arg | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288805 | p.Ala146Val | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326082 | c.1391dupA | frameshift_variant | 1.0 | ethionamide, ethionamide |
gid | 4407830 | p.Gln125* | stop_gained | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7423 | p.Leu41Arg | missense_variant | 0.1 |
mshA | 576113 | p.Arg256Gly | missense_variant | 0.26 |
rpoC | 765008 | p.Leu547Val | missense_variant | 1.0 |
rpoC | 766085 | p.Pro906Ala | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
atpE | 1460992 | c.-53A>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473291 | n.1446G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168473 | c.2139dupC | frameshift_variant | 0.11 |
PPE35 | 2168681 | p.Phe644Leu | missense_variant | 0.12 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519071 | p.Asp319Glu | missense_variant | 0.19 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.21 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.57 |
fbiD | 3339746 | p.Ala210Gly | missense_variant | 0.33 |
whiB7 | 3568428 | c.252A>G | synonymous_variant | 0.31 |
alr | 3840764 | c.657G>C | synonymous_variant | 1.0 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246527 | p.Ala5Gly | missense_variant | 0.2 |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.23 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |