Run ID: SRR18593215
Sample name:
Date: 03-04-2023 19:56:32
Number of reads: 4559494
Percentage reads mapped: 97.58
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 | 0.96 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Asn | missense_variant | 0.73 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7566 | p.Asp89Asn | missense_variant | 0.89 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.11 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761139 | p.His445Asp | missense_variant | 0.88 | rifampicin |
rpoB | 761155 | p.Ser450Trp | missense_variant | 0.12 | rifampicin |
rrs | 1472751 | n.906A>G | non_coding_transcript_exon_variant | 0.13 | streptomycin |
tlyA | 1918064 | c.126_127dupGG | frameshift_variant | 0.14 | capreomycin |
katG | 2155169 | p.Ser315Arg | missense_variant | 0.83 | isoniazid |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.11 | ethambutol |
embB | 4248002 | p.Gln497Lys | missense_variant | 0.78 | ethambutol |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.86 | ethambutol |
ethA | 4326675 | c.788_798delTGTTCCTGAGC | frameshift_variant | 0.85 | ethionamide |
ethA | 4326721 | c.752dupG | frameshift_variant | 0.15 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6091 | c.852G>A | synonymous_variant | 0.96 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoB | 761231 | c.1425C>T | synonymous_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 | 0.98 |
fabG1 | 1673162 | c.-278T>C | upstream_gene_variant | 0.99 |
inhA | 1674283 | p.Val28Leu | missense_variant | 0.98 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 |
katG | 2155627 | p.Ala162Glu | missense_variant | 0.11 |
katG | 2156419 | c.-308C>A | upstream_gene_variant | 0.84 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288832 | p.His137Leu | missense_variant | 0.12 |
pncA | 2289040 | c.187_201dupGACTATTCCTCGTCG | conservative_inframe_insertion | 0.76 |
ahpC | 2726142 | c.-51G>A | upstream_gene_variant | 0.17 |
Rv2752c | 3065938 | p.Asp85Gly | missense_variant | 0.15 |
ald | 3086966 | p.Asp49Glu | missense_variant | 0.98 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3236c | 3612047 | p.Ala357Val | missense_variant | 0.99 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4326505 | c.969C>G | synonymous_variant | 0.95 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408139 | p.Tyr22Asn | missense_variant | 0.89 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |