Run ID: SRR6831939
Sample name:
Date: 04-04-2023 17:07:44
Number of reads: 651287
Percentage reads mapped: 99.55
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 |
lineage2.2.1 | 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 |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol |
ethA | 4326598 | c.-695_875del | frameshift_variant&start_lost | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5223 | c.-17A>G | upstream_gene_variant | 0.12 |
gyrB | 6333 | p.Pro365Leu | missense_variant | 0.22 |
gyrB | 7029 | p.Ala597Val | missense_variant | 0.15 |
gyrA | 7308 | p.Asp3Tyr | missense_variant | 0.21 |
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 | 575184 | c.-164G>A | upstream_gene_variant | 0.4 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 761406 | p.Val534Met | missense_variant | 1.0 |
rpoB | 761837 | p.Cys677* | stop_gained | 0.25 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764751 | p.Val461Ala | missense_variant | 0.15 |
rpoC | 767256 | p.Asp1296Val | 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 | 776384 | c.2097C>A | synonymous_variant | 0.33 |
mmpL5 | 777553 | p.Val310Met | missense_variant | 0.25 |
mmpL5 | 778041 | p.Ala147Val | missense_variant | 0.14 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302793 | c.-138A>T | upstream_gene_variant | 0.2 |
fbiC | 1305055 | p.Met709Val | missense_variant | 0.2 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
atpE | 1461183 | p.Gly47Trp | missense_variant | 0.22 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473772 | n.115C>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474873 | n.1216G>T | non_coding_transcript_exon_variant | 0.17 |
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 | 2168412 | p.Phe734Ser | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3878707 | c.-200C>T | upstream_gene_variant | 0.18 |
clpC1 | 4039087 | p.Lys540Glu | missense_variant | 0.29 |
clpC1 | 4039195 | p.Thr504Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245296 | c.2064G>C | synonymous_variant | 0.15 |
embB | 4248056 | p.Ser515Gly | missense_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ubiA | 4269897 | c.-64C>T | upstream_gene_variant | 0.25 |
ethA | 4328464 | c.-991C>A | upstream_gene_variant | 0.22 |
whiB6 | 4338220 | p.Arg101His | missense_variant | 0.22 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338505 | p.Ala6Glu | missense_variant | 0.4 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.67 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
gid | 4408406 | c.-204A>G | upstream_gene_variant | 0.17 |