Run ID: ERR4829940
Sample name:
Date: 01-04-2023 19:46:42
Number of reads: 2288611
Percentage reads mapped: 99.66
Strain: lineage4;lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.22 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.79 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Ile | missense_variant | 0.32 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761095 | p.Leu430Arg | missense_variant | 0.25 | rifampicin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.24 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.79 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.75 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288850 | c.391dupG | frameshift_variant | 0.24 | pyrazinamide, pyrazinamide |
pncA | 2289231 | p.Leu4Ser | missense_variant | 0.75 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4327328 | c.145dupC | frameshift_variant | 0.33 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6061 | p.Ser274Arg | missense_variant | 0.76 |
gyrB | 6735 | p.Asn499Ser | missense_variant | 0.68 |
gyrB | 7210 | p.Asp657Glu | missense_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7581 | p.Asp94Ser | missense_variant | 0.6 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.28 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.21 |
rpoB | 759628 | c.-179C>T | upstream_gene_variant | 0.73 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.19 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.24 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407255 | p.Ala29Glu | missense_variant | 0.8 |
rrs | 1471653 | n.-193C>T | upstream_gene_variant | 0.3 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1673393 | c.-809G>A | upstream_gene_variant | 0.86 |
inhA | 1673431 | c.-771G>A | upstream_gene_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.21 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.27 |
PPE35 | 2169779 | c.834A>C | synonymous_variant | 0.83 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289256 | c.-15A>C | upstream_gene_variant | 0.83 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.22 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.28 |
Rv2752c | 3065855 | p.Ala113Pro | missense_variant | 0.21 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.24 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.24 |
fprA | 3474299 | p.Asp98Gly | missense_variant | 0.61 |
fprA | 3474367 | p.Gly121Ser | missense_variant | 0.75 |
panD | 4043957 | p.Asp109Asn | missense_variant | 0.72 |
panD | 4044399 | c.-118C>T | upstream_gene_variant | 0.28 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
aftB | 4268003 | c.834G>A | synonymous_variant | 0.29 |
ethA | 4328317 | c.-844C>T | upstream_gene_variant | 0.78 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.24 |
gid | 4408009 | c.193delG | frameshift_variant | 0.24 |