Run ID: SRR18003001
Sample name:
Date: 03-04-2023 19:13:42
Number of reads: 4133600
Percentage reads mapped: 99.15
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 | 7581 | p.Asp94Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288778 | p.Val155Gly | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4327189 | c.280_284dupATCGA | frameshift_variant | 0.99 | ethionamide |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.24 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
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 |
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 |
rrs | 1472192 | n.347G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472385 | n.540C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472789 | n.944G>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472808 | n.963C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472814 | n.969G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472980 | n.1135G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474749 | n.1092C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475600 | n.1943C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475698 | n.2041G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475967 | n.2310C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476378 | n.2721C>T | non_coding_transcript_exon_variant | 0.12 |
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 | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3065002 | p.His397Arg | 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 |
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 | 0.13 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.14 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.15 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.15 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.24 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.22 |
aftB | 4267351 | p.Met496Leu | missense_variant | 0.99 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ubiA | 4269361 | p.Leu158Ser | 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 |