Run ID: ERR234583
Sample name:
Date: 21-10-2023 13:09:00
Number of reads: 6746356
Percentage reads mapped: 99.54
Strain: lineage4.2.1;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Val (0.14) |
Isoniazid | R | inhA c.-154G>A (0.13), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (0.22) |
Pyrazinamide | R | pncA p.Tyr41* (0.20) |
Streptomycin | R | rpsL p.Lys43Arg (0.84), rrs n.906A>G (0.16) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | R | rrs n.1402C>T (0.16) |
Amikacin | R | rrs n.1402C>T (0.16) |
Capreomycin | R | rrs n.1402C>T (0.16) |
Kanamycin | R | rrs n.1402C>T (0.16) |
Cycloserine | ||
Ethionamide | R | inhA c.-154G>A (0.13), ethA c.1303delA (0.14), ethA c.987_999delAGGTCGCGAACTG (0.78) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.82 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.18 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.17 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.83 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.82 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.18 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761110 | p.Asp435Val | missense_variant | 0.14 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.84 | streptomycin |
rrs | 1472751 | n.906A>G | non_coding_transcript_exon_variant | 0.16 | streptomycin |
rrs | 1473247 | n.1402C>T | non_coding_transcript_exon_variant | 0.16 | kanamycin, capreomycin, aminoglycosides, amikacin |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.13 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289119 | p.Tyr41* | stop_gained | 0.2 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.22 | ethambutol |
ethA | 4326170 | c.1303delA | frameshift_variant | 0.14 | ethionamide |
ethA | 4326474 | c.987_999delAGGTCGCGAACTG | frameshift_variant | 0.78 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491247 | c.465C>T | synonymous_variant | 0.16 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.82 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.83 |
ccsA | 619969 | p.Val27Ile | missense_variant | 0.15 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.84 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.83 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.86 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.84 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.78 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.82 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.82 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.76 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.78 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.86 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726754 | p.Gly188Ser | missense_variant | 0.83 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.16 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.87 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.8 |
embA | 4245187 | p.Thr652Lys | missense_variant | 0.88 |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.84 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.23 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.8 |
gid | 4407713 | p.Gly164Arg | missense_variant | 0.27 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.82 |