Run ID: ERR4828444
Sample name:
Date: 20-10-2023 13:50:05
Number of reads: 1496741
Percentage reads mapped: 99.43
Strain: lineage2.2.1;lineage1.1.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.55) |
Isoniazid | R | katG p.Ser315Thr (0.42) |
Ethambutol | R | embB p.Met306Val (0.53) |
Pyrazinamide | R | pncA p.His71Tyr (0.39) |
Streptomycin | R | rpsL p.Lys88Arg (0.70) |
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 | 0.52 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.47 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.48 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.56 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.49 |
lineage1.1.1 | Indo-Oceanic | EAI4;EAI5 | RD239 | 0.43 |
lineage1.1.1.1 | Indo-Oceanic | EAI4;ZERO | RD239 | 0.53 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.55 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.7 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.42 | isoniazid |
pncA | 2289031 | p.His71Tyr | missense_variant | 0.39 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.53 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.35 |
gyrA | 7342 | p.Arg14Leu | missense_variant | 0.36 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.66 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490972 | p.Arg64Ser | missense_variant | 0.33 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.48 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.48 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.37 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.36 |
rpoC | 764942 | p.His525Asn | missense_variant | 0.47 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.37 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.57 |
mmpL5 | 777581 | p.Tyr300* | stop_gained | 0.52 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.5 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406588 | c.753C>T | synonymous_variant | 0.57 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.37 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 0.48 |
inhA | 1674210 | c.9A>C | synonymous_variant | 0.64 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.53 |
rpsA | 1834319 | p.Val260Ile | missense_variant | 0.26 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.95 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.33 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.53 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289446 | c.-205G>T | upstream_gene_variant | 0.67 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.53 |
eis | 2715081 | p.Phe84Leu | missense_variant | 0.64 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.45 |
folC | 2746905 | p.Ala232Thr | missense_variant | 0.46 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.43 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.56 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.58 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.56 |
fbiB | 3641625 | p.Ala31Thr | missense_variant | 0.45 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.62 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.52 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.45 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.43 |
embA | 4243848 | p.Val206Met | missense_variant | 0.49 |
embA | 4244096 | c.864C>T | synonymous_variant | 0.49 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.48 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.54 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.6 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.43 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.35 |
whiB6 | 4338242 | p.Gln94Glu | missense_variant | 0.62 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.34 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.41 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.44 |