Run ID: SRR6257024
Sample name:
Date: 04-04-2023 13:23:26
Number of reads: 718206
Percentage reads mapped: 99.66
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
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 |
---|---|---|---|---|---|
gyrB | 6750 | p.Ala504Val | missense_variant | 0.15 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764948 | p.Leu527Val | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288953 | p.Gly97Ser | missense_variant | 1.0 | pyrazinamide |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6579 | p.Ser447Tyr | missense_variant | 0.11 |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 759668 | c.-139A>G | upstream_gene_variant | 0.14 |
rpoB | 759783 | c.-24C>T | upstream_gene_variant | 0.14 |
rpoB | 759934 | p.Glu43Val | missense_variant | 0.22 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765571 | c.2202C>T | synonymous_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475747 | n.2090A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475761 | n.2104C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476693 | n.3036G>A | non_coding_transcript_exon_variant | 0.11 |
fabG1 | 1674149 | p.Ile237Asn | missense_variant | 0.1 |
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 | 2167831 | c.2782C>T | synonymous_variant | 0.11 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170254 | p.Leu120Pro | missense_variant | 0.14 |
PPE35 | 2170697 | c.-85T>C | upstream_gene_variant | 0.18 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726746 | p.Leu185Gln | missense_variant | 0.15 |
folC | 2746267 | c.1332C>A | synonymous_variant | 0.12 |
ald | 3086726 | c.-94C>A | upstream_gene_variant | 0.12 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449794 | c.1291C>T | synonymous_variant | 0.11 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.95 |
Rv3236c | 3612280 | c.837C>A | synonymous_variant | 0.13 |
Rv3236c | 3612404 | p.Ala238Val | missense_variant | 0.12 |
Rv3236c | 3612425 | p.Ala231Gly | missense_variant | 0.12 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
ddn | 3986665 | c.-179G>A | upstream_gene_variant | 0.1 |
ddn | 3987118 | p.Leu92Pro | missense_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243336 | p.Pro35Gln | missense_variant | 0.66 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267246 | p.Asn531Asp | missense_variant | 0.11 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327480 | c.-7T>G | upstream_gene_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | 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 |