Run ID: ERR2516727
Sample name:
Date: 31-03-2023 21:41:58
Number of reads: 963503
Percentage reads mapped: 99.59
Strain: lineage2.2.1.1
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 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 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 |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673432 | c.-8T>C | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
ahpC | 2726141 | c.-52C>T | upstream_gene_variant | 0.19 | isoniazid |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.22 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326213 | p.Arg421* | stop_gained | 0.14 | ethionamide |
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 | 490865 | p.Glu28Gly | missense_variant | 0.11 |
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 | 760983 | p.Val393Met | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775939 | p.Ala848Ser | missense_variant | 0.11 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 777999 | p.Leu161Pro | missense_variant | 0.13 |
mmpL5 | 778923 | c.-443C>T | upstream_gene_variant | 0.17 |
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 | 1471864 | n.19A>G | non_coding_transcript_exon_variant | 0.12 |
fabG1 | 1673512 | c.78dupG | frameshift_variant | 0.17 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102693 | p.Val117Ala | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154857 | p.Asp419Tyr | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168561 | c.2052T>C | synonymous_variant | 0.1 |
PPE35 | 2168772 | p.Leu614Ser | missense_variant | 0.12 |
Rv1979c | 2221743 | c.1422T>C | synonymous_variant | 0.1 |
Rv1979c | 2222912 | p.Ala85Thr | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288772 | p.Val157Ala | missense_variant | 0.23 |
pncA | 2288959 | p.Tyr95Asp | missense_variant | 1.0 |
pncA | 2289098 | c.144G>A | synonymous_variant | 0.12 |
eis | 2714447 | c.886T>C | synonymous_variant | 0.12 |
eis | 2714846 | p.Val163Ile | missense_variant | 1.0 |
ahpC | 2726775 | p.Ala195Ser | missense_variant | 0.11 |
pepQ | 2860502 | c.-84A>G | upstream_gene_variant | 0.11 |
ribD | 2986894 | p.Ser19Leu | missense_variant | 0.12 |
ribD | 2987473 | p.Cys212Tyr | missense_variant | 0.14 |
thyA | 3073840 | p.Asn211Ser | missense_variant | 0.12 |
ald | 3086745 | c.-75G>A | upstream_gene_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339127 | p.Thr4Pro | missense_variant | 0.11 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3877960 | p.Val183Gly | missense_variant | 1.0 |
clpC1 | 4038702 | p.Leu668Pro | missense_variant | 0.11 |
clpC1 | 4040501 | c.204C>T | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244992 | p.Val587Ala | missense_variant | 0.11 |
embB | 4248115 | c.1602C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4269810 | c.-974A>G | upstream_gene_variant | 0.22 |
ethA | 4327065 | p.Cys137Arg | missense_variant | 0.36 |
ethR | 4327976 | p.Gln143Arg | missense_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338600 | c.-79T>C | upstream_gene_variant | 0.12 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |