Run ID: ERR2653102
Sample name:
Date: 31-03-2023 22:31:22
Number of reads: 574146
Percentage reads mapped: 99.47
Strain: lineage4.7
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 |
lineage4.7 | Euro-American (mainly T) | T1;T5 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.92 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764948 | p.Leu527Val | missense_variant | 0.67 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6259 | c.1020C>T | synonymous_variant | 0.1 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 9458 | c.2157A>G | synonymous_variant | 0.1 |
mshA | 575896 | c.549G>A | synonymous_variant | 0.13 |
ccsA | 620852 | p.Ala321Val | missense_variant | 0.12 |
rpoB | 759940 | p.Pro45Leu | missense_variant | 0.41 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775715 | c.2766G>A | synonymous_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474428 | n.771C>T | non_coding_transcript_exon_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918059 | c.120C>A | synonymous_variant | 0.25 |
Rv1979c | 2222097 | c.1068G>A | synonymous_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289070 | p.Phe58Val | missense_variant | 1.0 |
ribD | 2987346 | p.Pro170Ser | missense_variant | 0.11 |
fbiD | 3339652 | p.Thr179Ala | missense_variant | 0.11 |
alr | 3841071 | p.Gly117Asp | missense_variant | 1.0 |
rpoA | 3878601 | c.-95delG | upstream_gene_variant | 0.59 |
clpC1 | 4040525 | c.180C>T | synonymous_variant | 1.0 |
embC | 4241591 | p.Leu577Ile | missense_variant | 0.1 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243977 | p.Ala249Thr | missense_variant | 1.0 |
embB | 4249732 | c.3219C>G | synonymous_variant | 1.0 |
ethA | 4327521 | c.-48G>A | upstream_gene_variant | 0.12 |
ethA | 4327523 | c.-50G>C | upstream_gene_variant | 0.12 |
ethA | 4327525 | c.-52T>C | upstream_gene_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407590 | p.Ala205Thr | missense_variant | 1.0 |