Run ID: SRR26159062
Sample name:
Date: 16-03-2024 13:37:19
Number of reads: 1030283
Percentage reads mapped: 99.02
Strain:
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.37), rpoB p.Ile491Phe (0.48) |
Isoniazid | R | katG p.Ser315Thr (0.58) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.58) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.55 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.48 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.51 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.37 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.37 | rifampicin |
rpoB | 761277 | p.Ile491Phe | missense_variant | 0.48 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.58 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.58 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.6 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.33 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.4 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.31 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.33 |
rpoC | 766809 | p.Val1147Ala | missense_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.58 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.61 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.52 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.35 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2103137 | c.-95A>G | upstream_gene_variant | 0.44 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.52 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.44 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289910 | c.-669C>T | upstream_gene_variant | 0.61 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.31 |
Rv2752c | 3064889 | p.Lys435Glu | missense_variant | 0.43 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.7 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.61 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.34 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.5 |
fbiA | 3641404 | p.Trp288Arg | missense_variant | 0.29 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.47 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.57 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.45 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.62 |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.35 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.82 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.47 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.62 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.27 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.66 |
whiB6 | 4338635 | c.-114A>C | upstream_gene_variant | 0.61 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.59 |
gid | 4407898 | c.273_305delAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGinsC | frameshift_variant&missense_variant | 0.57 |
gid | 4407898 | p.Glu92Asp | missense_variant | 0.43 |