Run ID: SRR23862005
Sample name:
Date: 12-04-2023 14:25:25
Number of reads: 2888770
Percentage reads mapped: 99.55
Strain: lineage4.2.1;lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.73) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.72) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.29 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.74 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.26 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.2 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.75 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.72 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.73 | isoniazid |
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 | 0.34 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.21 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.17 |
mshA | 576453 | p.Val369Gly | missense_variant | 0.21 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.29 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.24 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.31 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.33 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.3 |
mmpL5 | 777883 | p.Gly200Arg | missense_variant | 0.19 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.27 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.25 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.24 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.27 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.18 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.71 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519006 | p.Ala298Ser | missense_variant | 0.24 |
kasA | 2519071 | p.Asp319Glu | missense_variant | 0.17 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.21 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.76 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.8 |
Rv3083 | 3448456 | c.-48G>A | upstream_gene_variant | 0.77 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568428 | c.252A>G | synonymous_variant | 0.3 |
whiB7 | 3568431 | c.249C>G | synonymous_variant | 0.38 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.33 |
rpoA | 3878590 | c.-83G>C | upstream_gene_variant | 0.29 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.67 |
clpC1 | 4038932 | c.1773G>A | synonymous_variant | 0.82 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.29 |
embB | 4246527 | p.Ala5Gly | missense_variant | 0.2 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.29 |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.75 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.24 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.77 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.27 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.33 |