Run ID: SRR25827529
Sample name:
Date: 02-02-2024 08:40:58
Number of reads: 9202890
Percentage reads mapped: 99.22
Strain: lineage4.8;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.16), rpoB p.Leu452Pro (0.85) |
Isoniazid | R | fabG1 c.-15C>T (0.22), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Leu (0.75), embB p.Gln497Arg (0.23) |
Pyrazinamide | R | pncA p.Gly132Ala (0.20), pncA p.Gln10Pro (0.74) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.25) |
Moxifloxacin | R | gyrA p.Ala90Val (0.25) |
Ofloxacin | R | gyrA p.Ala90Val (0.25) |
Levofloxacin | R | gyrA p.Ala90Val (0.25) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.25) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | R | eis c.-10G>C (0.21), eis c.-10G>C (0.21) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.22) |
Clofazimine | ||
Para-aminosalicylic_acid | R | thyX c.-16C>T (0.22) |
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.22 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.78 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.21 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.79 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.23 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.25 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.16 | rifampicin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.85 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.22 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.2 | pyrazinamide |
pncA | 2289213 | p.Gln10Pro | missense_variant | 0.74 | pyrazinamide |
eis | 2715342 | c.-10G>C | upstream_gene_variant | 0.21 | kanamycin, kanamycin |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.22 | para-aminosalicylic_acid |
embB | 4247429 | p.Met306Leu | missense_variant | 0.75 | ethambutol |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.23 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.24 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.23 |
fgd1 | 491290 | p.Val170Met | missense_variant | 0.25 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.19 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.17 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.21 |
rpoB | 760315 | p.Val170Ala | missense_variant | 0.82 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.25 |
rpoC | 764840 | p.Ile491Val | missense_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.22 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.22 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.85 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.2 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.18 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.88 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.25 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.24 |
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.13 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.23 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.77 |
embC | 4241022 | p.Ala387Val | missense_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.19 |
embB | 4247015 | p.Ser168Ala | missense_variant | 0.13 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.23 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.23 |
gid | 4407620 | p.Tyr195His | missense_variant | 0.22 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.19 |