Run ID: SRR6384965
Sample name:
Date: 04-04-2023 13:42:14
Number of reads: 1740500
Percentage reads mapped: 91.02
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 | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.45 | streptomycin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.61 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.29 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.67 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.98 | isoniazid |
pncA | 2289054 | p.Asp63Ala | missense_variant | 0.39 | pyrazinamide |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.57 | pyrazinamide |
ddn | 3987106 | p.Trp88* | stop_gained | 0.34 | delamanid |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.65 | ethambutol |
embB | 4247513 | p.Tyr334His | missense_variant | 0.54 | ethambutol |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.52 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 7209 | p.Asp657Gly | missense_variant | 0.45 |
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 | 576482 | p.Val379Leu | missense_variant | 0.12 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.71 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.78 |
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 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.11 |
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 |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.14 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.42 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087532 | p.Ala238Asp | missense_variant | 0.73 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.31 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612229 | c.888C>T | synonymous_variant | 0.5 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3877956 | p.Glu184Asp | missense_variant | 0.36 |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 0.45 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.22 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.39 |
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 |