Run ID: ERR12544380
Sample name:
Date: 22-02-2024 21:40:57
Number of reads: 3446001
Percentage reads mapped: 99.66
Strain: lineage4.1.2.1;lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.11) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.36) |
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 | 0.28 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.68 |
lineage4.1 | Euro-American | T;X;H | None | 0.64 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.33 |
lineage4.1.2 | Euro-American | T;H | None | 0.66 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.32 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.67 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.36 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.11 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5713 | c.474C>G | synonymous_variant | 0.47 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.98 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.73 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.45 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.67 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.3 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.18 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.65 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.27 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.66 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.32 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.38 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.37 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.32 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.32 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474428 | n.771C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474438 | n.781A>G | non_coding_transcript_exon_variant | 0.11 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.25 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.41 |
PPE35 | 2167792 | p.Ser941Ala | missense_variant | 0.66 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.38 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.75 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612660 | p.Ser153Ala | missense_variant | 0.36 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.3 |
rpoA | 3878567 | c.-60C>G | upstream_gene_variant | 0.28 |
rpoA | 3878599 | c.-92C>G | upstream_gene_variant | 0.13 |
rpoA | 3878627 | c.-120T>G | upstream_gene_variant | 0.12 |
rpoA | 3878639 | c.-132C>G | upstream_gene_variant | 0.24 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.62 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.3 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.17 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.21 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.19 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.19 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.18 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.33 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.98 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.43 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.45 |
gid | 4408436 | c.-234C>T | upstream_gene_variant | 0.65 |