Run ID: SRR5149238
Sample name:
Date: 04-04-2023 09:09:35
Number of reads: 494471
Percentage reads mapped: 92.3
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.92 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.92 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.84 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6737 | p.Thr500Pro | missense_variant | 0.9 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.67 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.91 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.93 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.11 | isoniazid, ethionamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.54 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.89 | 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 | 7892 | c.591G>A | synonymous_variant | 0.25 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.14 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.22 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.94 |
rpoB | 759615 | c.-192A>C | upstream_gene_variant | 0.27 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 767123 | p.Val1252Met | missense_variant | 0.92 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775694 | p.Ile929Met | missense_variant | 0.92 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.83 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.33 |
mmpL5 | 777160 | p.Ala441Ser | missense_variant | 0.15 |
mmpL5 | 777390 | p.Phe364Cys | missense_variant | 0.15 |
mmpL5 | 778447 | c.24_33dupGCCGACGGGC | frameshift_variant | 0.33 |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.67 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.9 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800802 | c.-7C>T | upstream_gene_variant | 0.2 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.82 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472012 | n.167A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474961 | n.1304T>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476141 | n.2484A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476165 | n.2508T>G | non_coding_transcript_exon_variant | 0.14 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.15 |
fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.87 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102578 | p.Phe155Leu | missense_variant | 0.18 |
katG | 2154086 | p.Gly676Arg | missense_variant | 1.0 |
katG | 2154217 | p.Arg632His | missense_variant | 0.85 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155935 | c.177T>G | synonymous_variant | 0.29 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.91 |
PPE35 | 2168711 | c.1902A>G | synonymous_variant | 0.17 |
Rv1979c | 2222042 | p.Thr375Pro | missense_variant | 0.22 |
Rv1979c | 2222532 | c.633C>A | synonymous_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289028 | p.Cys72Gly | missense_variant | 0.87 |
pncA | 2289786 | c.-545G>T | upstream_gene_variant | 0.13 |
ribD | 2987259 | p.Leu141Val | missense_variant | 0.67 |
Rv2752c | 3065129 | c.1063C>T | synonymous_variant | 0.92 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.94 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568594 | p.Phe29Cys | missense_variant | 0.22 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3612971 | p.Leu49Trp | missense_variant | 0.29 |
fbiB | 3640647 | c.-888G>T | upstream_gene_variant | 0.25 |
embC | 4240026 | p.Thr55Asn | missense_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4248004 | p.Gln497His | missense_variant | 0.71 |
embB | 4248005 | p.Thr498Ser | missense_variant | 0.71 |
embB | 4249305 | p.Asn931Thr | missense_variant | 0.29 |
aftB | 4266974 | c.1863C>A | synonymous_variant | 0.2 |
aftB | 4267190 | c.1647T>G | synonymous_variant | 0.2 |
aftB | 4267240 | p.Phe533Val | missense_variant | 0.14 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.8 |
ethA | 4326617 | p.Tyr286Ser | missense_variant | 0.18 |
ethR | 4326658 | c.-891T>G | upstream_gene_variant | 0.33 |
ethA | 4326676 | p.Ser266Arg | missense_variant | 0.73 |
ethR | 4327688 | p.Val47Gly | missense_variant | 0.15 |
ethR | 4327695 | p.Asp49Glu | missense_variant | 0.15 |
ethR | 4327697 | p.Leu50Arg | missense_variant | 0.17 |
whiB6 | 4338326 | p.Ala66Thr | missense_variant | 0.67 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.7 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.89 |