Run ID: ERR067738
Sample name:
Date: 31-03-2023 09:08:01
Number of reads: 4398662
Percentage reads mapped: 99.58
Strain: lineage4.3.3;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.69 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.3 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.27 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.74 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.71 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.26 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 0.25 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.69 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.71 | streptomycin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.26 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.3 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 0.65 | kanamycin |
folC | 2747151 | p.Ser150Gly | missense_variant | 0.73 | para-aminosalicylic_acid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.72 | ethambutol |
embB | 4247729 | p.Gly406Cys | missense_variant | 0.3 | 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 | 8040 | p.Gly247Ser | missense_variant | 0.29 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.64 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.68 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.67 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.8 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.71 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.29 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.71 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.69 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.67 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.77 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303095 | c.165G>A | synonymous_variant | 0.42 |
fbiC | 1304962 | p.Trp678Gly | missense_variant | 0.3 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.61 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.74 |
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.27 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.74 |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.31 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.73 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.27 |
folC | 2746340 | p.Ala420Val | missense_variant | 0.3 |
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 0.24 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.27 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.2 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.29 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.72 |
rpoA | 3877981 | p.Tyr176Cys | missense_variant | 0.14 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.35 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.2 |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 0.25 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.24 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.99 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.68 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.73 |
ethA | 4326761 | p.Val238Gly | missense_variant | 0.71 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.7 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.82 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.29 |