Run ID: SRR11972187
Sample name:
Date: 03-04-2023 05:31:24
Number of reads: 459148
Percentage reads mapped: 92.19
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 | 2289213 | p.Gln10Pro | missense_variant | 1.0 | pyrazinamide |
embB | 4247357 | p.Val282Leu | missense_variant | 0.14 | ethambutol |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6584 | p.Asp449Asn | missense_variant | 0.11 |
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 | 761161 | c.1359delG | frameshift_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764058 | p.Ala230Val | missense_variant | 1.0 |
rpoC | 764881 | c.1512G>A | synonymous_variant | 0.15 |
rpoC | 764938 | c.1569G>A | synonymous_variant | 0.15 |
rpoC | 765462 | p.Asn698Ser | missense_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 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472634 | n.789T>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 | 0.16 |
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472982 | n.1137G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1474226 | n.569A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476359 | n.2702C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476481 | n.2824T>C | 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 |
tlyA | 1918472 | p.Val178Ala | missense_variant | 0.1 |
katG | 2154591 | c.1521C>G | synonymous_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169113 | c.1500G>C | synonymous_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289347 | c.-106C>T | upstream_gene_variant | 0.12 |
pncA | 2289500 | c.-260delG | upstream_gene_variant | 0.15 |
folC | 2747437 | p.Met54Ile | missense_variant | 1.0 |
thyA | 3073908 | p.Met188Ile | missense_variant | 0.22 |
thyA | 3074283 | c.188delT | frameshift_variant | 0.11 |
ald | 3086645 | c.-175C>T | upstream_gene_variant | 0.13 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473851 | c.-156G>A | upstream_gene_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiA | 3641404 | p.Trp288Arg | missense_variant | 0.11 |
fbiB | 3642323 | c.789T>C | synonymous_variant | 0.2 |
rpoA | 3877766 | p.Ala248Pro | missense_variant | 0.13 |
clpC1 | 4040119 | p.Glu196Gln | missense_variant | 0.11 |
embC | 4241958 | p.Arg699Leu | missense_variant | 1.0 |
embC | 4242593 | p.His911Tyr | missense_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245017 | c.1785C>T | synonymous_variant | 0.12 |
embB | 4249051 | c.2538C>G | synonymous_variant | 0.1 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267661 | c.1176G>C | synonymous_variant | 0.11 |
ethR | 4326940 | c.-609G>T | upstream_gene_variant | 0.22 |
ethA | 4327164 | p.Val104Met | missense_variant | 0.17 |
whiB6 | 4338425 | p.Val33Ile | missense_variant | 1.0 |
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 |