Run ID: ERR12268447
Sample name:
Date: 11-01-2024 09:48:05
Number of reads: 2564014
Percentage reads mapped: 99.7
Strain: lineage4.3.1;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Phe (0.41) |
Isoniazid | R | katG p.Ser315Thr (0.61) |
Ethambutol | R | embB p.Met306Val (0.47) |
Pyrazinamide | R | pncA p.Trp68Arg (0.35) |
Streptomycin | R | rpsL p.Lys43Arg (0.72) |
Fluoroquinolones | R | gyrA p.Asp94Asn (0.17) |
Moxifloxacin | R | gyrA p.Asp94Asn (0.17) |
Ofloxacin | R | gyrA p.Asp94Asn (0.17) |
Levofloxacin | R | gyrA p.Asp94Asn (0.17) |
Ciprofloxacin | R | gyrA p.Asp94Asn (0.17) |
Aminoglycosides | R | rrs n.1401A>G (0.59) |
Amikacin | R | rrs n.1401A>G (0.59) |
Capreomycin | R | rrs n.1401A>G (0.59) |
Kanamycin | R | rrs n.1401A>G (0.59) |
Cycloserine | ||
Ethionamide | R | ethA c.489dupT (0.33) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.42 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.52 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.54 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.46 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.44 |
lineage4.3.1 | Euro-American (LAM) | LAM9 | None | 0.41 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Asn | missense_variant | 0.17 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Phe | missense_variant | 0.41 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.72 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.59 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.61 | isoniazid |
pncA | 2289040 | p.Trp68Arg | missense_variant | 0.35 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.47 | ethambutol |
ethA | 4326984 | c.489dupT | frameshift_variant | 0.33 | 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 | 491742 | c.960T>C | synonymous_variant | 0.66 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.44 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.54 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.45 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.39 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.49 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.49 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.37 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.5 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.54 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.48 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.35 |
PPE35 | 2168412 | p.Phe734Cys | missense_variant | 0.34 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.15 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.59 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.48 |
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 | 0.44 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.65 |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 0.23 |
embC | 4239965 | p.Val35Met | missense_variant | 0.16 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243222 | c.-11C>T | upstream_gene_variant | 0.16 |
embA | 4243346 | c.114A>G | synonymous_variant | 0.42 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.54 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.58 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.46 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.39 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.52 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.54 |