Run ID: ERR4799887
Sample name:
Date: 01-04-2023 09:26:50
Number of reads: 2855264
Percentage reads mapped: 99.58
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.97 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.95 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7581 | p.Asp94Asn | missense_variant | 0.95 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.95 | rifampicin |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.91 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.91 | streptomycin |
fabG1 | 1673432 | c.-8T>A | upstream_gene_variant | 0.88 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289228 | p.Ile5Ser | missense_variant | 0.95 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.94 | kanamycin |
thyA | 3074408 | p.Thr22Ala | missense_variant | 0.94 | para-aminosalicylic_acid |
alr | 3840393 | p.Met343Thr | missense_variant | 0.37 | cycloserine |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.95 | 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 | 491290 | p.Val170Met | missense_variant | 0.95 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.98 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.98 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.93 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.95 |
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 | 1472310 | n.465T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472527 | n.682G>T | non_coding_transcript_exon_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.97 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3065711 | p.Gly161Ser | missense_variant | 0.13 |
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.95 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086944 | p.Gly42Asp | missense_variant | 0.16 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embC | 4241022 | p.Ala387Val | missense_variant | 0.91 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4247847 | p.Gln445Arg | missense_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327283 | p.Phe64Ser | missense_variant | 0.95 |
whiB6 | 4338292 | p.Ala77Val | missense_variant | 0.92 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407620 | p.Tyr195His | missense_variant | 0.93 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.97 |