Run ID: ERR5863845
Sample name:
Date: 01-04-2023 22:56:45
Number of reads: 733467
Percentage reads mapped: 99.47
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 | 761078 | p.Phe424Leu | missense_variant | 0.14 | rifampicin |
rpoB | 761155 | p.Ser450Phe | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288820 | p.Gln141Pro | missense_variant | 1.0 | pyrazinamide |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6242 | p.Arg335Ser | missense_variant | 0.18 |
gyrB | 6447 | p.Ala403Glu | missense_variant | 0.22 |
gyrB | 6829 | p.Met530Ile | missense_variant | 0.18 |
gyrB | 6959 | p.Gln574* | stop_gained | 0.15 |
gyrB | 7082 | p.Glu615* | stop_gained | 0.15 |
gyrA | 7216 | c.-86G>T | upstream_gene_variant | 0.15 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7731 | p.Glu144* | stop_gained | 0.4 |
gyrA | 7745 | p.Glu148Asp | missense_variant | 0.17 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9394 | p.Ser698* | stop_gained | 0.2 |
gyrA | 9508 | p.Ala736Glu | missense_variant | 0.2 |
fgd1 | 491092 | p.Gly104Cys | missense_variant | 0.18 |
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 |
rpoC | 762923 | c.-447C>A | upstream_gene_variant | 0.14 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 767015 | p.Ala1216Thr | missense_variant | 0.14 |
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 | 1304635 | p.Gln569* | stop_gained | 0.19 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471704 | n.-142C>A | upstream_gene_variant | 0.17 |
rrs | 1472800 | n.955C>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474522 | n.865C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475625 | n.1969delT | non_coding_transcript_exon_variant | 0.67 |
inhA | 1674072 | c.-130C>A | upstream_gene_variant | 0.17 |
rpsA | 1834001 | p.Glu154* | stop_gained | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834191 | p.Ser217Tyr | missense_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102123 | p.Pro307His | missense_variant | 0.12 |
katG | 2154536 | p.Glu526* | stop_gained | 0.18 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154891 | c.1221G>A | synonymous_variant | 0.22 |
katG | 2155825 | p.Gly96Val | missense_variant | 0.15 |
PPE35 | 2167813 | p.Gln934Lys | missense_variant | 0.14 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168921 | c.1692G>A | synonymous_variant | 0.2 |
Rv1979c | 2222280 | c.885C>A | synonymous_variant | 0.17 |
Rv1979c | 2222641 | p.Ser175* | stop_gained | 0.5 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv1979c | 2223299 | c.-135G>T | upstream_gene_variant | 0.17 |
pncA | 2289960 | c.-719C>G | upstream_gene_variant | 0.15 |
kasA | 2518240 | c.126C>A | synonymous_variant | 0.2 |
ahpC | 2726716 | p.Ala175Glu | missense_variant | 0.13 |
ribD | 2986777 | c.-62C>A | upstream_gene_variant | 0.2 |
Rv2752c | 3065150 | c.1041_1042insA | frameshift_variant | 1.0 |
Rv2752c | 3067187 | c.-997_-996insG | upstream_gene_variant | 1.0 |
thyA | 3073815 | c.657G>A | synonymous_variant | 0.13 |
thyA | 3073855 | p.Cys206Phe | missense_variant | 0.14 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448342 | c.-162A>G | upstream_gene_variant | 0.12 |
Rv3083 | 3449116 | p.Ala205Ser | missense_variant | 0.15 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568757 | c.-78A>T | upstream_gene_variant | 0.13 |
Rv3236c | 3612289 | c.828G>T | synonymous_variant | 0.14 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3641130 | c.-405A>G | upstream_gene_variant | 0.11 |
alr | 3841453 | c.-33G>T | upstream_gene_variant | 0.17 |
rpoA | 3877867 | p.Thr214Met | missense_variant | 0.14 |
clpC1 | 4039864 | p.Asp281Tyr | missense_variant | 0.18 |
clpC1 | 4039915 | p.Asp264Tyr | missense_variant | 0.18 |
embC | 4239665 | c.-198G>A | upstream_gene_variant | 0.13 |
embC | 4240160 | p.Thr100Ser | missense_variant | 0.17 |
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 | 4246207 | p.Pro992Gln | missense_variant | 0.17 |
aftB | 4267320 | p.Asp506Gly | missense_variant | 0.13 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267915 | p.Pro308Thr | missense_variant | 0.15 |
ethA | 4326669 | p.Gln269Lys | missense_variant | 0.14 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407537 | c.666G>T | synonymous_variant | 0.18 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |