Run ID: SRR3085264
Sample name:
Date: 04-04-2023 04:56:05
Number of reads: 1953998
Percentage reads mapped: 99.36
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 | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289057 | p.Pro62Leu | missense_variant | 1.0 | pyrazinamide |
embB | 4247730 | p.Gly406Ala | missense_variant | 0.9 | ethambutol |
ethA | 4327363 | c.110delA | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5176 | c.-63_-62delGT | upstream_gene_variant | 0.5 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9543 | p.Lys748Glu | missense_variant | 0.15 |
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 |
ccsA | 620697 | c.807C>T | synonymous_variant | 0.12 |
ccsA | 620843 | p.His318Arg | missense_variant | 0.11 |
rpoB | 762250 | p.Leu815Pro | missense_variant | 0.12 |
rpoB | 762880 | p.Met1025Thr | missense_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764703 | p.Lys445Arg | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775847 | c.2634G>T | synonymous_variant | 0.4 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 778480 | c.1A>G | start_lost | 0.15 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800794 | c.-15A>G | upstream_gene_variant | 0.11 |
fbiC | 1304826 | c.1900delT | frameshift_variant | 0.18 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
Rv1258c | 1407145 | p.Val66Ile | missense_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1674901 | p.Asp234Asn | missense_variant | 0.12 |
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 |
katG | 2156204 | c.-93A>T | upstream_gene_variant | 0.13 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168088 | p.Pro842Leu | missense_variant | 0.11 |
PPE35 | 2169625 | p.Gly330Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519315 | p.Ser401Thr | missense_variant | 0.12 |
eis | 2715290 | p.Gly15Trp | missense_variant | 0.11 |
eis | 2715362 | c.-30T>C | upstream_gene_variant | 0.12 |
folC | 2746198 | c.1401C>G | synonymous_variant | 0.12 |
folC | 2747383 | c.216C>T | synonymous_variant | 0.15 |
folC | 2747513 | p.Gln29Arg | missense_variant | 0.12 |
pepQ | 2859755 | p.Phe222Ile | missense_variant | 0.12 |
pepQ | 2860205 | p.Glu72* | stop_gained | 0.1 |
Rv2752c | 3064605 | c.1587C>A | synonymous_variant | 0.14 |
thyA | 3073962 | c.510G>A | synonymous_variant | 0.11 |
thyA | 3074605 | c.-134T>G | upstream_gene_variant | 0.17 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448555 | p.Gly18Arg | missense_variant | 0.12 |
Rv3083 | 3448819 | p.Thr106Ala | missense_variant | 0.13 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841429 | c.-9T>C | upstream_gene_variant | 0.1 |
clpC1 | 4038701 | c.2004G>A | synonymous_variant | 0.11 |
clpC1 | 4039661 | c.1043dupG | frameshift_variant | 0.11 |
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 | 4244159 | c.927G>T | synonymous_variant | 0.4 |
embA | 4245681 | p.Gly817Ser | missense_variant | 0.12 |
embA | 4246437 | p.Ala1069Thr | missense_variant | 0.11 |
embB | 4248799 | c.2286T>C | synonymous_variant | 0.17 |
aftB | 4267528 | p.Ala437Ser | missense_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267742 | c.1095G>A | synonymous_variant | 0.12 |
ethA | 4328358 | c.-885C>T | upstream_gene_variant | 0.11 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407790 | p.Ala138Val | missense_variant | 0.11 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
gid | 4408186 | p.Pro6Leu | missense_variant | 0.18 |