Run ID: SRR6256992
Sample name:
Date: 04-04-2023 13:22:13
Number of reads: 1033813
Percentage reads mapped: 100.0
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-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 |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoB | 762089 | p.Glu761Asp | missense_variant | 1.0 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.25 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6937 | c.-365G>T | upstream_gene_variant | 0.14 |
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 | 575477 | p.Pro44Thr | missense_variant | 0.16 |
mshA | 575792 | p.Asp149Tyr | missense_variant | 0.29 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576750 | p.Lys468Thr | missense_variant | 0.15 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 759615 | c.-192A>C | upstream_gene_variant | 0.24 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763707 | p.Arg113Leu | missense_variant | 0.12 |
rpoC | 766645 | p.Glu1092Asp | 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 |
fbiC | 1303182 | p.Ile84Met | missense_variant | 0.11 |
fbiC | 1304976 | p.Lys682Asn | missense_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476309 | n.2652G>T | non_coding_transcript_exon_variant | 0.12 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102496 | p.Val183Phe | missense_variant | 0.2 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.25 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222435 | p.Glu244* | stop_gained | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714335 | p.Ile333Thr | missense_variant | 0.12 |
eis | 2714560 | p.Gly258Val | missense_variant | 0.14 |
eis | 2714981 | p.Leu118Met | missense_variant | 0.14 |
eis | 2715498 | c.-166G>T | upstream_gene_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339605 | p.Gly163Val | missense_variant | 0.15 |
Rv3083 | 3448901 | p.Cys133Phe | missense_variant | 0.13 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474225 | p.Asp73Glu | missense_variant | 0.12 |
Rv3236c | 3611994 | p.Gly375Ser | missense_variant | 0.14 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3878634 | c.-127C>T | upstream_gene_variant | 0.5 |
rpoA | 3878646 | c.-139G>T | upstream_gene_variant | 0.2 |
clpC1 | 4039483 | p.Ala408Ser | missense_variant | 0.13 |
embC | 4240653 | p.Pro264Leu | missense_variant | 0.29 |
embC | 4242354 | p.Gly831Val | missense_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244521 | p.Ala430Asp | missense_variant | 0.12 |
embA | 4244533 | p.Thr434Ser | missense_variant | 0.12 |
embB | 4249332 | p.Pro940His | missense_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267889 | c.948C>G | synonymous_variant | 0.1 |
whiB6 | 4338563 | c.-42G>T | upstream_gene_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 |