Run ID: SRR5527200
Sample name:
Date: 04-04-2023 10:36:52
Number of reads: 575933
Percentage reads mapped: 99.62
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 |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
inhA | 1674262 | p.Ile21Val | missense_variant | 1.0 | isoniazid |
pncA | 2289040 | p.Trp68Arg | missense_variant | 1.0 | pyrazinamide |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | 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 | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 759746 | c.-61C>G | upstream_gene_variant | 0.12 |
rpoB | 761118 | p.Asn438Asp | missense_variant | 0.1 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764027 | p.Glu220* | stop_gained | 0.14 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
rpoC | 766533 | p.Leu1055Pro | missense_variant | 0.11 |
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 |
rpsL | 781501 | c.-59C>G | upstream_gene_variant | 0.11 |
fbiC | 1303842 | c.912C>T | synonymous_variant | 0.2 |
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 | 0.17 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102738 | c.304delG | frameshift_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170440 | p.Gln58Pro | missense_variant | 0.4 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518398 | p.Trp95Leu | missense_variant | 0.11 |
kasA | 2518864 | c.750G>C | synonymous_variant | 0.12 |
kasA | 2519365 | c.1251A>G | stop_lost&splice_region_variant | 0.1 |
eis | 2714846 | p.Val163Ile | missense_variant | 1.0 |
folC | 2747486 | p.Trp38* | stop_gained | 0.17 |
folC | 2747776 | c.-178G>T | upstream_gene_variant | 0.12 |
Rv2752c | 3065000 | p.Gly398Arg | missense_variant | 0.11 |
thyA | 3074313 | c.159A>G | synonymous_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339349 | p.Asp78Asn | missense_variant | 0.12 |
Rv3083 | 3448319 | c.-185C>A | upstream_gene_variant | 0.15 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3613255 | c.-139G>A | upstream_gene_variant | 0.11 |
fbiB | 3642473 | p.Met313Ile | missense_variant | 0.2 |
clpC1 | 4040228 | c.477G>A | synonymous_variant | 0.13 |
embC | 4242255 | p.Pro798Arg | missense_variant | 0.15 |
embC | 4242557 | p.Gln899Lys | missense_variant | 0.25 |
embC | 4242632 | p.Pro924Thr | missense_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245131 | c.1899G>A | synonymous_variant | 1.0 |
embB | 4248115 | c.1602C>T | synonymous_variant | 1.0 |
embB | 4248558 | p.Tyr682Ser | missense_variant | 0.13 |
aftB | 4267645 | p.Asp398His | missense_variant | 0.14 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethR | 4327589 | p.Gly14Val | missense_variant | 0.11 |
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 |