Run ID: ERR4798955
Sample name:
Date: 20-10-2023 03:26:54
Number of reads: 3944353
Percentage reads mapped: 99.6
Strain: lineage4.1.2.1;lineage3;lineage2.2.1.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.29) |
Ethambutol | R | embB p.Met306Val (0.18) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.20) |
Fluoroquinolones | R | gyrA p.Asp94Gly (0.12) |
Moxifloxacin | R | gyrA p.Asp94Gly (0.12) |
Ofloxacin | R | gyrA p.Asp94Gly (0.12) |
Levofloxacin | R | gyrA p.Asp94Gly (0.12) |
Ciprofloxacin | R | gyrA p.Asp94Gly (0.12) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.14 |
lineage2 | East-Asian | Beijing | RD105 | 0.2 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.67 |
lineage4.1 | Euro-American | T;X;H | None | 0.62 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.2 |
lineage4.1.2 | Euro-American | T;H | None | 0.61 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.17 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.65 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.12 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.12 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.2 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.29 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 0.18 | 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 | 491591 | p.Lys270Met | missense_variant | 0.67 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.39 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.52 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.17 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.23 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.14 |
rpoB | 760061 | c.255C>T | synonymous_variant | 0.63 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.64 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.17 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.41 |
rpoC | 764363 | p.Gly332Ser | missense_variant | 0.19 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.62 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.37 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.15 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.2 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302920 | c.-11G>A | upstream_gene_variant | 0.74 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673204 | c.-236C>T | upstream_gene_variant | 0.16 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.16 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.36 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.36 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288755 | p.Val163Met | missense_variant | 0.67 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.15 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.15 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.58 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.16 |
fbiB | 3641490 | c.-45G>A | upstream_gene_variant | 0.62 |
rpoA | 3878586 | c.-79A>G | upstream_gene_variant | 0.32 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.6 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.19 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.23 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.32 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.16 |