Run ID: SRR1048872
Sample name:
Date: 02-04-2023 17:49:14
Number of reads: 3273116
Percentage reads mapped: 98.6
Strain: lineage2.2.2
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 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761097 | p.Ser431Arg | missense_variant | 0.31 | rifampicin |
rpoB | 761155 | p.Ser450Trp | 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 | 0.98 | kanamycin, capreomycin, aminoglycosides, amikacin |
embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6674 | p.Leu479Ile | missense_variant | 1.0 |
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 |
rpoB | 761547 | p.Val581Leu | missense_variant | 0.69 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475953 | n.2296A>C | non_coding_transcript_exon_variant | 0.42 |
rrl | 1475954 | n.2297A>G | non_coding_transcript_exon_variant | 0.34 |
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 |
katG | 2155418 | p.Pro232Ser | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.98 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3064550 | p.Gln548* | stop_gained | 0.17 |
Rv2752c | 3064966 | p.Leu409Arg | missense_variant | 0.67 |
Rv2752c | 3065092 | p.Gln367Arg | missense_variant | 1.0 |
thyA | 3073762 | p.Ser237Leu | missense_variant | 1.0 |
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 | 3841562 | c.-142A>G | upstream_gene_variant | 0.98 |
clpC1 | 4039592 | c.1113G>A | synonymous_variant | 0.98 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327292 | p.Thr61Lys | missense_variant | 1.0 |
whiB6 | 4338592 | c.-71G>C | upstream_gene_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 |