Run ID: SRR11972157
Sample name:
Date: 03-04-2023 05:30:15
Number of reads: 466610
Percentage reads mapped: 99.15
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 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289040 | p.Trp68Arg | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
embB | 4249583 | p.Asp1024Asn | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6545 | p.Gly436Cys | missense_variant | 0.18 |
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 | 760816 | p.Glu337Gly | missense_variant | 0.5 |
rpoB | 761420 | c.1614C>T | synonymous_variant | 0.18 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763082 | c.-288C>T | upstream_gene_variant | 0.15 |
rpoC | 764058 | p.Ala230Val | missense_variant | 1.0 |
rpoC | 764817 | p.Val483Ala | missense_variant | 1.0 |
rpoC | 765096 | p.Met576Lys | missense_variant | 0.17 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 777608 | c.873C>T | synonymous_variant | 0.33 |
mmpL5 | 778972 | c.-492G>A | upstream_gene_variant | 0.22 |
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 |
rrs | 1472193 | n.348A>G | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.57 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472373 | n.528G>A | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.29 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.15 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.15 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.15 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.4 |
fabG1 | 1673526 | c.87_88insT | frameshift_variant | 0.22 |
inhA | 1674546 | p.Asp115Glu | missense_variant | 0.29 |
rpsA | 1833736 | c.195C>T | synonymous_variant | 0.15 |
rpsA | 1833738 | p.Arg66His | missense_variant | 0.17 |
rpsA | 1833832 | c.291G>A | synonymous_variant | 0.13 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918171 | p.Ala78Thr | missense_variant | 0.29 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167865 | c.2748G>C | synonymous_variant | 0.19 |
PPE35 | 2167868 | c.2745A>C | synonymous_variant | 0.19 |
PPE35 | 2167878 | p.Ser912Asn | missense_variant | 0.14 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169351 | p.Ala421Gly | missense_variant | 0.12 |
PPE35 | 2169363 | p.Ile417Thr | missense_variant | 0.12 |
PPE35 | 2169884 | c.729T>C | synonymous_variant | 0.11 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.44 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.57 |
PPE35 | 2170288 | p.Leu109Val | missense_variant | 0.12 |
PPE35 | 2170308 | p.Leu102Ala | missense_variant | 0.12 |
PPE35 | 2170313 | c.300G>C | synonymous_variant | 0.13 |
PPE35 | 2170403 | c.210C>G | synonymous_variant | 0.18 |
PPE35 | 2170406 | c.207A>G | synonymous_variant | 0.18 |
Rv1979c | 2222968 | p.Ala66Val | missense_variant | 0.22 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.2 |
folC | 2746180 | c.1419C>A | synonymous_variant | 0.29 |
folC | 2747437 | p.Met54Ile | missense_variant | 1.0 |
ribD | 2986950 | p.Gly38Ser | missense_variant | 0.17 |
ribD | 2987587 | p.Tyr250Cys | missense_variant | 0.25 |
thyA | 3074648 | c.-177T>G | upstream_gene_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087309 | p.Pro164Ala | missense_variant | 0.12 |
ald | 3087369 | p.Ala184Pro | missense_variant | 0.14 |
fprA | 3473952 | c.-55C>T | upstream_gene_variant | 0.33 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642427 | p.Val298Ala | missense_variant | 0.18 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.14 |
clpC1 | 4039508 | c.1197G>C | synonymous_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244575 | p.Ala448Val | missense_variant | 0.17 |
embB | 4246052 | c.-462C>A | upstream_gene_variant | 0.33 |
embB | 4246824 | p.Lys104Arg | missense_variant | 0.11 |
embB | 4247461 | p.Met316Ile | missense_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethR | 4327087 | c.-462G>T | upstream_gene_variant | 0.25 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338605 | c.-84C>T | upstream_gene_variant | 0.17 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |