Run ID: ERR108422
Sample name:
Date: 31-03-2023 11:17:08
Number of reads: 5186088
Percentage reads mapped: 99.56
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 | 0.13 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.89 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.88 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.12 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.12 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.88 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.86 | rifampicin |
rpoB | 762089 | p.Glu761Asp | missense_variant | 0.18 | rifampicin |
fabG1 | 1673432 | c.-8T>A | upstream_gene_variant | 0.89 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.88 | ethambutol |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 0.14 | ethionamide |
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 | 0.83 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.15 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.13 |
rpoB | 761172 | p.Gly456Ser | missense_variant | 0.88 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.14 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.84 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.13 |
rpoC | 766667 | p.Ser1100Ala | missense_variant | 0.86 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.11 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.11 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.17 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.19 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918681 | p.Asp248Cys | missense_variant | 0.9 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.13 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289226 | p.Ile6Leu | missense_variant | 0.12 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.9 |
pepQ | 2860571 | c.-153T>G | upstream_gene_variant | 0.9 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.27 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.89 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339490 | p.Leu125Ile | missense_variant | 0.86 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.16 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.85 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.26 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244823 | p.Val531Leu | missense_variant | 0.86 |
embB | 4248316 | c.1803C>T | synonymous_variant | 0.91 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.19 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407877 | p.Gly109Ala | missense_variant | 0.91 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.88 |