Run ID: SRR1723689
Sample name:
Date: 12-08-2022 17:11:47
Number of reads: 3173510
Percentage reads mapped: 93.86
Strain: lineage2.2.1.1
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 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6621 | p.Asp461Ala | missense_variant | 0.78 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.99 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
pncA | 2288950 | c.281_291delTCTACAAGGGT | frameshift_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | 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 | 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 | 764389 | p.Leu340Phe | missense_variant | 1.0 |
rpoC | 767314 | p.Tyr1315* | stop_gained | 0.42 |
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 | 0.98 |
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 | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.09 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.11 |
inhA | 1674952 | p.Pro251Ala | missense_variant | 0.33 |
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 | 2156217 | c.-106G>C | upstream_gene_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714846 | p.Val163Ile | 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 | 4247495 | p.Asp328His | missense_variant | 1.0 |
embB | 4248115 | c.1602C>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 |