Run ID: ERR8025622
Sample name:
Date: 18-05-2023 03:44:09
Number of reads: 2799643
Percentage reads mapped: 99.6
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | R | pncA p.Thr160Ala (1.00), pncA p.Thr100Ile (1.00) |
Streptomycin | R | rrs n.514A>C (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
Aminoglycosides | R | rrs n.1401A>G (1.00) |
Amikacin | R | rrs n.1401A>G (1.00) |
Capreomycin | R | rrs n.1401A>G (1.00) |
Kanamycin | R | rrs n.1401A>G (1.00) |
Cycloserine | R | ald c.464delG (0.17) |
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288764 | p.Thr160Ala | missense_variant | 1.0 | pyrazinamide |
pncA | 2288943 | p.Thr100Ile | missense_variant | 1.0 | pyrazinamide |
ald | 3087278 | c.464delG | frameshift_variant | 0.17 | cycloserine |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
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 | 491328 | c.546C>G | synonymous_variant | 1.0 |
fgd1 | 491330 | p.Lys183Met | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575719 | c.372C>T | synonymous_variant | 0.13 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 761015 | c.1209G>A | synonymous_variant | 0.13 |
rpoB | 763021 | p.Ala1072Asp | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764822 | p.Asp485Tyr | missense_variant | 1.0 |
mmpL5 | 775592 | c.2889G>A | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 777934 | p.Lys183Glu | missense_variant | 0.11 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
Rv1258c | 1407465 | c.-125G>A | upstream_gene_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472609 | n.764G>T | non_coding_transcript_exon_variant | 0.33 |
rpsA | 1834159 | c.618G>A | synonymous_variant | 0.17 |
rpsA | 1834168 | c.627C>T | synonymous_variant | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519118 | p.Ala335Glu | missense_variant | 0.11 |
eis | 2714351 | p.Arg328Trp | missense_variant | 0.11 |
ahpC | 2726108 | c.-85A>G | upstream_gene_variant | 0.1 |
folC | 2746386 | p.His405Asn | missense_variant | 0.17 |
ribD | 2986921 | p.Leu28Pro | missense_variant | 0.11 |
ribD | 2987614 | c.776G>C | stop_lost&splice_region_variant | 0.13 |
Rv2752c | 3064565 | p.Glu543Lys | missense_variant | 0.13 |
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086846 | c.32dupA | frameshift_variant | 0.48 |
ald | 3087658 | c.840dupG | frameshift_variant | 0.36 |
Rv3083 | 3449315 | p.Trp271* | stop_gained | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612484 | c.633T>C | synonymous_variant | 0.11 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3641583 | p.Val17Ile | missense_variant | 0.12 |
alr | 3840994 | p.His143Tyr | missense_variant | 0.11 |
alr | 3841340 | c.81G>A | synonymous_variant | 0.15 |
embC | 4242417 | p.Gly852Asp | missense_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245015 | p.Ile595Val | missense_variant | 0.11 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethR | 4326655 | c.-894G>A | upstream_gene_variant | 0.14 |
ethA | 4326713 | p.Gln254Pro | missense_variant | 1.0 |
whiB6 | 4338365 | p.Cys53Arg | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |