Run ID: SRR11972350
Sample name:
Date: 03-04-2023 05:38:16
Number of reads: 2355799
Percentage reads mapped: 98.79
Strain: lineage2.2.1
Drug-resistance: MDR-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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.95 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.98 | ethambutol |
embB | 4249583 | p.Asp1024Asn | 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 |
rpoB | 761773 | p.His656Pro | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
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 |
fbiC | 1304449 | p.Ala507Thr | missense_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472128 | n.283G>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472151 | n.306C>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472708 | n.863T>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472803 | n.958T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472953 | n.1108G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1474218 | n.561T>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474228 | n.571T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474252 | n.595T>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474256 | n.599T>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474733 | n.1076C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475218 | n.1561C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.13 |
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 | 2170159 | p.Ala152Ser | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2859592 | p.Ala276Glu | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475007 | p.Phe334Ser | missense_variant | 0.12 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
clpC1 | 4038253 | p.Phe818Leu | missense_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.29 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.24 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.37 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.38 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.21 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4328315 | c.-842C>T | upstream_gene_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338600 | c.-79T>G | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |