Run ID: ERR2515304
Sample name:
Date: 31-03-2023 20:51:47
Number of reads: 728918
Percentage reads mapped: 93.55
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
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 | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.96 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.91 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
inhA | 1674782 | p.Ile194Thr | missense_variant | 1.0 | isoniazid, ethionamide |
pncA | 2289220 | p.Asp8Asn | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethR | 4327831 | p.Ala95Thr | missense_variant | 1.0 | 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 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763555 | c.186C>T | synonymous_variant | 0.93 |
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 | 778979 | c.-74G>T | upstream_gene_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304658 | c.1728C>G | synonymous_variant | 0.12 |
fbiC | 1304660 | p.Tyr577Phe | missense_variant | 0.12 |
fbiC | 1304664 | c.1734G>C | synonymous_variant | 0.12 |
fbiC | 1304671 | p.Val581Thr | missense_variant | 0.12 |
fbiC | 1304676 | c.1746A>C | synonymous_variant | 0.12 |
fbiC | 1304691 | c.1761G>T | synonymous_variant | 0.12 |
fbiC | 1304694 | c.1764A>G | synonymous_variant | 0.12 |
fbiC | 1304715 | c.1785G>C | synonymous_variant | 0.15 |
fbiC | 1304724 | c.1794A>G | synonymous_variant | 0.15 |
fbiC | 1304727 | c.1797A>C | synonymous_variant | 0.14 |
fbiC | 1304742 | c.1812T>C | synonymous_variant | 0.16 |
fbiC | 1304751 | c.1821C>G | synonymous_variant | 0.17 |
fbiC | 1304757 | c.1827A>G | synonymous_variant | 0.19 |
fbiC | 1304760 | c.1830G>C | synonymous_variant | 0.19 |
fbiC | 1304769 | c.1839C>G | synonymous_variant | 0.19 |
fbiC | 1304781 | c.1851G>C | synonymous_variant | 0.15 |
fbiC | 1304784 | c.1854T>C | synonymous_variant | 0.15 |
fbiC | 1304790 | c.1860C>G | synonymous_variant | 0.14 |
fbiC | 1304811 | c.1881C>G | synonymous_variant | 0.14 |
fbiC | 1304817 | c.1887T>C | synonymous_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472446 | n.601T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472452 | n.607G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472456 | n.611T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474969 | n.1312G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475062 | n.1405A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475479 | n.1822C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476251 | n.2594T>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476281 | n.2624T>C | 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 | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_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 |
rpoA | 3878103 | c.405A>G | synonymous_variant | 0.12 |
clpC1 | 4039979 | c.726C>G | synonymous_variant | 0.11 |
clpC1 | 4040009 | c.696C>G | synonymous_variant | 0.12 |
clpC1 | 4040015 | c.690G>C | synonymous_variant | 0.12 |
clpC1 | 4040021 | c.684A>C | synonymous_variant | 0.13 |
clpC1 | 4040024 | c.681A>G | synonymous_variant | 0.13 |
clpC1 | 4040033 | c.672G>T | synonymous_variant | 0.12 |
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 |
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 |