Run ID: ERR11082857
Sample name:
Date: 11-04-2023 09:14:48
Number of reads: 5219672
Percentage reads mapped: 99.69
Strain: lineage4.3.4.1;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.58) |
Isoniazid | R | ahpC c.-57C>T (0.57) |
Ethambutol | R | embB p.Met306Val (0.61) |
Pyrazinamide | R | pncA p.Ala171Glu (0.61) |
Streptomycin | R | rpsL p.Lys43Arg (0.48) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | R | folC p.Ser150Gly (0.59) |
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.56 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.4 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.44 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.6 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.57 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.39 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 0.43 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.58 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.48 | streptomycin |
pncA | 2288730 | p.Ala171Glu | missense_variant | 0.61 | pyrazinamide |
ahpC | 2726136 | c.-57C>T | upstream_gene_variant | 0.57 | isoniazid |
folC | 2747151 | p.Ser150Gly | missense_variant | 0.59 | para-aminosalicylic_acid |
embB | 4247429 | p.Met306Val | missense_variant | 0.61 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5602 | c.363C>T | synonymous_variant | 0.42 |
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 | 0.57 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.54 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.34 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.55 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.47 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.34 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.54 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.57 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.54 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.6 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.59 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.63 |
rpsA | 1834427 | p.Ile296Val | missense_variant | 0.62 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102092 | c.951G>A | synonymous_variant | 0.45 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.77 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.42 |
Rv1979c | 2222854 | p.Ile104Thr | missense_variant | 0.42 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073680 | c.792A>G | stop_lost&splice_region_variant | 0.62 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.46 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449346 | c.843G>A | synonymous_variant | 0.46 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.44 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.58 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.44 |
clpC1 | 4039991 | c.714G>A | synonymous_variant | 0.5 |
panD | 4043867 | p.Gly139* | stop_gained | 0.56 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.53 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.41 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.5 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.55 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.53 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.42 |