Run ID: ERR5897084
Sample name:
Date: 02-04-2023 00:47:53
Number of reads: 13804461
Percentage reads mapped: 99.5
Strain: lineage4.9;lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.4 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.6 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 0.6 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.65 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.33 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.98 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.62 | streptomycin |
rrs | 1472723 | n.878G>A | non_coding_transcript_exon_variant | 0.13 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.62 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.26 | isoniazid, ethionamide |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.65 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288883 | p.Leu120Arg | missense_variant | 0.31 | pyrazinamide |
pncA | 2289081 | p.Pro54Leu | missense_variant | 0.59 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.94 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.34 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.4 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.39 |
mshA | 576400 | c.1053C>T | synonymous_variant | 0.61 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.41 |
rpoB | 759786 | c.-21G>C | upstream_gene_variant | 0.11 |
rpoB | 761461 | p.Arg552Leu | missense_variant | 0.65 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.4 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.43 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.28 |
rpoC | 766582 | c.3213C>A | synonymous_variant | 0.28 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.4 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918272 | c.333C>T | synonymous_variant | 0.3 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.36 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.38 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.41 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.4 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.43 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.4 |
ald | 3086987 | p.Gln56His | missense_variant | 0.59 |
ald | 3087367 | p.Ala183Val | missense_variant | 0.55 |
ald | 3087604 | p.Ala262Glu | missense_variant | 0.63 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.39 |
alr | 3841473 | c.-53G>A | upstream_gene_variant | 0.4 |
rpoA | 3877536 | c.972C>T | synonymous_variant | 0.61 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.42 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.39 |
ubiA | 4269124 | p.Ala237Val | missense_variant | 0.61 |
whiB6 | 4338307 | p.Ala72Gly | missense_variant | 0.65 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.39 |
gid | 4407790 | p.Ala138Val | missense_variant | 0.23 |