Run ID: SRR25827668
Sample name:
Date: 02-02-2024 14:22:14
Number of reads: 6792235
Percentage reads mapped: 99.1
Strain: lineage3.1.2;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.86) |
Isoniazid | R | fabG1 c.-15C>T (0.82), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Gln497Arg (0.92) |
Pyrazinamide | R | pncA p.Gly132Ala (0.77) |
Streptomycin | R | rpsL p.Lys43Arg (0.82) |
Fluoroquinolones | R | gyrA p.Asp94Gly (0.79) |
Moxifloxacin | R | gyrA p.Asp94Gly (0.79) |
Ofloxacin | R | gyrA p.Asp94Gly (0.79) |
Levofloxacin | R | gyrA p.Asp94Gly (0.79) |
Ciprofloxacin | R | gyrA p.Asp94Gly (0.79) |
Aminoglycosides | R | rrs n.1401A>G (0.81) |
Amikacin | R | rrs n.1401A>G (0.81) |
Capreomycin | R | rrs n.1401A>G (0.81) |
Kanamycin | R | rrs n.1401A>G (0.81) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.82) |
Clofazimine | ||
Para-aminosalicylic_acid | R | thyX c.-16C>T (0.83) |
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.2 |
lineage2 | East-Asian | Beijing | RD105 | 0.83 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.81 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.12 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.81 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.79 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.86 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.82 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.81 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.82 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.77 | pyrazinamide |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.83 | para-aminosalicylic_acid |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.92 | ethambutol |
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 | 491290 | p.Val170Met | missense_variant | 0.81 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.89 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.84 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.2 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.16 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764840 | p.Ile491Val | missense_variant | 0.82 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.82 |
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 | 0.79 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.81 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.18 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.18 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.18 |
thyA | 3073987 | p.Gln162Pro | missense_variant | 0.81 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087647 | c.830dupG | frameshift_variant | 0.81 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.15 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.83 |
alr | 3841540 | c.-120T>C | upstream_gene_variant | 0.8 |
embC | 4241022 | p.Ala387Val | missense_variant | 0.81 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.21 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.82 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.21 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.84 |
aftB | 4268753 | c.84T>G | synonymous_variant | 0.8 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407620 | p.Tyr195His | missense_variant | 0.86 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.83 |