Run ID: ERR2510682
Sample name:
Date: 31-03-2023 18:53:33
Number of reads: 2370531
Percentage reads mapped: 98.35
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 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.28 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.69 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
katG | 2155892 | p.Asp74Tyr | missense_variant | 0.15 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247513 | p.Tyr334His | missense_variant | 0.88 | ethambutol |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 619784 | c.-107G>A | upstream_gene_variant | 0.12 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.95 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
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 |
mmpL5 | 777128 | c.1353A>G | synonymous_variant | 0.14 |
mmpL5 | 777262 | p.Thr407Ala | missense_variant | 0.14 |
mmpL5 | 777263 | c.1218G>C | synonymous_variant | 0.14 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303965 | c.1035G>A | synonymous_variant | 0.13 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474828 | n.1172delC | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475154 | n.1497C>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475175 | n.1518G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.14 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.2 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102074 | p.Met323Lys | missense_variant | 0.12 |
ndh | 2102604 | c.439T>C | synonymous_variant | 0.13 |
ndh | 2102610 | c.433T>C | synonymous_variant | 0.12 |
ndh | 2102875 | c.168C>T | synonymous_variant | 0.16 |
katG | 2153970 | p.Asp714Glu | missense_variant | 0.14 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167865 | c.2748G>C | synonymous_variant | 0.19 |
PPE35 | 2167868 | c.2745A>C | synonymous_variant | 0.18 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.13 |
PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.13 |
PPE35 | 2169269 | c.1344A>G | synonymous_variant | 0.15 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.12 |
PPE35 | 2169293 | c.1320T>C | synonymous_variant | 0.12 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.2 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.12 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.14 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.15 |
PPE35 | 2170147 | p.Ser156Ala | missense_variant | 0.42 |
PPE35 | 2170157 | p.Ala152Ser | missense_variant | 0.2 |
PPE35 | 2170308 | p.Leu102Ala | missense_variant | 0.12 |
PPE35 | 2170313 | c.300G>C | synonymous_variant | 0.11 |
PPE35 | 2170349 | c.264C>A | synonymous_variant | 0.22 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289361 | c.-125delC | upstream_gene_variant | 0.12 |
folC | 2746174 | c.1425A>G | synonymous_variant | 0.12 |
ribD | 2987211 | p.Arg125Ser | missense_variant | 0.14 |
thyA | 3074514 | c.-43T>C | upstream_gene_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087532 | p.Ala238Asp | missense_variant | 1.0 |
Rv3083 | 3449049 | c.546C>G | synonymous_variant | 0.18 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612229 | c.888C>T | synonymous_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3612965 | p.Val51Glu | missense_variant | 0.18 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.22 |
clpC1 | 4039714 | p.Tyr331His | missense_variant | 0.18 |
clpC1 | 4039730 | c.975C>G | synonymous_variant | 0.22 |
clpC1 | 4040057 | c.648C>T | synonymous_variant | 0.23 |
clpC1 | 4040087 | c.618G>T | synonymous_variant | 0.16 |
clpC1 | 4040090 | c.615T>C | synonymous_variant | 0.16 |
clpC1 | 4040093 | c.612C>G | synonymous_variant | 0.17 |
clpC1 | 4040144 | c.561G>C | synonymous_variant | 0.14 |
embC | 4240475 | p.Ala205Thr | missense_variant | 0.14 |
embC | 4242217 | c.2355C>T | synonymous_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4244247 | p.Val339Ile | missense_variant | 0.12 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.22 |
embB | 4247090 | p.Thr193Ala | missense_variant | 0.14 |
embB | 4247098 | c.585C>G | synonymous_variant | 0.12 |
embB | 4247512 | c.999T>C | synonymous_variant | 0.12 |
embB | 4247516 | p.Asn335Asp | missense_variant | 0.11 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4267935 | p.Val301Ala | missense_variant | 0.12 |
ethR | 4327633 | p.Ile29Phe | missense_variant | 0.15 |
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 |