Run ID: ERR12328176
Sample name:
Date: 12-03-2024 16:48:37
Number of reads: 2159793
Percentage reads mapped: 99.34
Strain: lineage1.2.1.2.1;lineage1.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.42) |
Isoniazid | R | fabG1 c.-15C>T (0.22) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | R | rrs n.1401A>G (0.26) |
Amikacin | R | rrs n.1401A>G (0.26) |
Capreomycin | R | rrs n.1401A>G (0.26) |
Kanamycin | R | rrs n.1401A>G (0.26) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.22) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.25 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 | 0.25 |
lineage1.2.1 | Indo-Oceanic | EAI2 | RD239 | 0.73 |
lineage1.2.1.2 | Indo-Oceanic | NA | RD239 | 0.76 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 0.72 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.42 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.26 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.22 | isoniazid, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.98 |
gyrA | 6472 | c.-830G>T | upstream_gene_variant | 0.76 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9260 | c.1959G>C | synonymous_variant | 0.69 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575368 | c.21T>C | synonymous_variant | 0.72 |
rpoB | 760386 | p.His194Tyr | missense_variant | 0.32 |
rpoB | 760750 | p.Gly315Glu | missense_variant | 0.68 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763531 | c.162G>C | synonymous_variant | 0.79 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.19 |
rpoC | 765191 | p.Glu608Gln | missense_variant | 0.21 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 778116 | p.His122Arg | missense_variant | 0.25 |
mmpR5 | 779053 | p.Gln22* | stop_gained | 0.32 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 0.82 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 0.75 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 0.26 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 0.67 |
rpsA | 1834319 | p.Val260Ile | missense_variant | 0.27 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.29 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289524 | c.-283C>T | upstream_gene_variant | 0.82 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 0.78 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726070 | c.-123G>A | upstream_gene_variant | 0.33 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.33 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 0.77 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fprA | 3475302 | c.1296C>T | synonymous_variant | 0.19 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 0.76 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 0.61 |
alr | 3840260 | c.1161C>T | synonymous_variant | 0.71 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243580 | c.348G>A | synonymous_variant | 0.68 |
embA | 4243848 | p.Val206Met | missense_variant | 0.25 |
embA | 4244096 | c.864C>T | synonymous_variant | 0.25 |
embA | 4244420 | c.1188G>C | synonymous_variant | 0.67 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247578 | c.1065G>A | synonymous_variant | 0.65 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248409 | c.1896A>G | synonymous_variant | 0.76 |
ubiA | 4269152 | p.Ala228Ser | missense_variant | 0.26 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 0.79 |
ethA | 4327483 | c.-10G>A | upstream_gene_variant | 0.28 |
whiB6 | 4338242 | p.Gln94Glu | missense_variant | 0.16 |
whiB6 | 4338361 | p.Arg54Gln | missense_variant | 0.75 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |