Run ID: ERR4831991
Sample name:
Date: 01-04-2023 21:15:18
Number of reads: 396988
Percentage reads mapped: 99.21
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 |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.33 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761140 | p.His445Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.87 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288853 | c.380_388delAGGTCGATG | disruptive_inframe_deletion | 0.8 | pyrazinamide |
folC | 2747151 | p.Ser150Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7136 | c.-166T>C | upstream_gene_variant | 0.4 |
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 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765951 | p.Ala861Val | missense_variant | 0.7 |
rpoC | 766171 | c.2802C>A | synonymous_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775821 | c.2659delG | frameshift_variant | 0.2 |
mmpL5 | 776037 | c.2443delT | frameshift_variant | 0.17 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 776323 | p.Ile720Phe | missense_variant | 0.18 |
mmpL5 | 777202 | p.Ala427Thr | missense_variant | 0.13 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781361 | c.-199G>T | upstream_gene_variant | 0.15 |
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 |
rrs | 1473282 | n.1437C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474919 | n.1262A>G | non_coding_transcript_exon_variant | 0.18 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.13 |
fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.13 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.32 |
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 | 2167654 | p.Pro987Thr | missense_variant | 0.22 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168882 | c.1731T>C | synonymous_variant | 0.22 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.62 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.62 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyX | 3067340 | c.606G>A | synonymous_variant | 0.18 |
thyX | 3067676 | c.270C>T | synonymous_variant | 0.12 |
thyA | 3074191 | p.Tyr94Ser | missense_variant | 0.13 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 0.8 |
ddn | 3986857 | p.Pro5Leu | missense_variant | 0.22 |
clpC1 | 4038996 | c.1707_1708delCT | frameshift_variant | 0.17 |
clpC1 | 4040809 | c.-105G>T | upstream_gene_variant | 0.33 |
embC | 4241565 | p.Ile568Thr | missense_variant | 0.4 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.27 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.22 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.2 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.2 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.2 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.25 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4326337 | p.Asn379Lys | 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 |