Run ID: ERR9992908
Sample name:
Date: 02-04-2023 13:55:14
Number of reads: 4095574
Percentage reads mapped: 99.82
Strain: lineage4.3.3;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.14 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.85 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.8 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.14 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.16 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.82 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Gly | missense_variant | 0.81 | rifampicin |
rpoB | 761114 | c.1312_1314delAAC | conservative_inframe_deletion | 0.12 | rifampicin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.82 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.88 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.13 | isoniazid, ethionamide |
fabG1 | 1673432 | c.-8T>A | upstream_gene_variant | 0.86 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.85 | isoniazid |
pncA | 2288785 | c.456dupC | frameshift_variant | 0.81 | pyrazinamide, pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.8 | ethambutol |
ethA | 4327484 | c.-11A>G | upstream_gene_variant | 0.82 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6575 | p.Arg446Gly | missense_variant | 0.78 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.82 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.12 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.13 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.21 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.14 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.14 |
rpoB | 763123 | p.Ile1106Thr | missense_variant | 0.82 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.83 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.12 |
mmpR5 | 779237 | p.Leu83Pro | missense_variant | 0.15 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 0.81 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154023 | p.Val697Phe | missense_variant | 0.13 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.17 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.17 |
Rv1979c | 2223051 | p.Glu38Asp | missense_variant | 0.76 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.79 |
pepQ | 2859478 | c.931_940delACATCCGCCG | frameshift_variant | 0.1 |
pepQ | 2859874 | c.544dupG | frameshift_variant | 0.11 |
pepQ | 2860119 | c.299dupA | frameshift_variant | 0.56 |
Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 0.79 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.79 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087895 | c.1081dupG | frameshift_variant | 0.8 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.19 |
alr | 3841147 | p.Ala92Thr | missense_variant | 0.81 |
rpoA | 3878630 | c.-123G>C | upstream_gene_variant | 0.14 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.78 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.16 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.14 |
embB | 4249563 | p.Asp1017Ala | missense_variant | 0.14 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.1 |
ubiA | 4269271 | p.Val188Ala | missense_variant | 0.82 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.16 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.82 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.78 |