Run ID: SRR22424931
Sample name:
Date: 04-04-2023 04:17:18
Number of reads: 905912
Percentage reads mapped: 77.68
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 | 0.98 |
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 | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
tlyA | 1918194 | c.257_258delGT | frameshift_variant | 1.0 | capreomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288697 | p.Leu182Ser | missense_variant | 1.0 | pyrazinamide |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6180 | p.Gly314Asp | missense_variant | 0.12 |
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 |
ccsA | 619922 | p.Ala11Val | missense_variant | 0.18 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764363 | p.Gly332Ser | missense_variant | 1.0 |
rpoC | 764430 | p.Leu354Pro | missense_variant | 0.12 |
rpoC | 767122 | c.3753C>T | synonymous_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 778362 | p.Leu40Ser | missense_variant | 0.12 |
mmpR5 | 779154 | p.Glu55Asp | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801021 | c.213C>T | synonymous_variant | 1.0 |
fbiC | 1305494 | c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT | frameshift_variant&stop_lost&splice_region_variant | 0.4 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472236 | n.391C>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472697 | n.852T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472779 | n.934G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474252 | n.595T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475843 | n.2186G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476297 | n.2640C>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.49 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.15 |
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 |
Rv2752c | 3065453 | p.Gln247* | stop_gained | 1.0 |
thyX | 3067286 | c.660C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474939 | c.933G>A | synonymous_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841393 | p.Lys10Glu | missense_variant | 0.11 |
clpC1 | 4040752 | c.-49_-48insTACG | upstream_gene_variant | 0.13 |
embC | 4240969 | c.1107C>T | synonymous_variant | 0.11 |
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 |
aftB | 4268050 | p.Pro263Ser | missense_variant | 0.11 |
ethA | 4326676 | p.Ser266Arg | missense_variant | 1.0 |
ethA | 4327208 | p.Ala89Glu | missense_variant | 1.0 |
whiB6 | 4338276 | c.246C>T | synonymous_variant | 0.12 |
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 |
gid | 4408352 | c.-150C>T | upstream_gene_variant | 0.12 |
fbiC | 1305494 | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | frameshift_variant&stop_lost&splice_region_variant | 1.0 |