Run ID: ERR4800367
Sample name:
Date: 20-10-2023 04:20:17
Number of reads: 3479858
Percentage reads mapped: 99.58
Strain: lineage4.8;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.39) |
Isoniazid | R | katG p.Ser315Thr (0.98) |
Ethambutol | R | embB p.Met306Val (0.35) |
Pyrazinamide | R | pncA p.Asp63Gly (0.26) |
Streptomycin | R | rpsL p.Lys43Arg (0.33), rrs n.906A>G (0.77), gid c.102delG (0.77) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64) |
Moxifloxacin | R | gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64) |
Ofloxacin | R | gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64) |
Levofloxacin | R | gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64) |
Aminoglycosides | R | rrs n.1401A>G (0.23) |
Amikacin | R | rrs n.1401A>G (0.23) |
Capreomycin | R | rrs n.1401A>G (0.23) |
Kanamycin | R | rrs n.1401A>G (0.23) |
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.73 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.3 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.68 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.29 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.66 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.28 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7581 | p.Asp94Asn | missense_variant | 0.64 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.39 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.33 | streptomycin |
rrs | 1472751 | n.906A>G | non_coding_transcript_exon_variant | 0.77 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.23 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.98 | isoniazid |
pncA | 2289054 | p.Asp63Gly | missense_variant | 0.26 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.35 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 0.77 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5332 | c.93C>T | synonymous_variant | 0.34 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.68 |
gyrA | 8168 | p.Glu289Asp | missense_variant | 0.3 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.58 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.65 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.77 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.72 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.71 |
rpoC | 765862 | p.Phe831Leu | missense_variant | 0.35 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.69 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.68 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.7 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406738 | c.603C>T | synonymous_variant | 0.72 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.68 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.2 |
inhA | 1673406 | c.-796C>G | upstream_gene_variant | 0.31 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.61 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.62 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.73 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.26 |
PPE35 | 2169424 | p.Ser397Pro | missense_variant | 0.71 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
folC | 2747470 | p.Ile43Ala | missense_variant | 0.29 |
Rv2752c | 3065773 | p.Glu140Gly | missense_variant | 0.33 |
Rv2752c | 3067039 | c.-848T>C | upstream_gene_variant | 0.64 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.71 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.69 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.65 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.29 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.74 |
embA | 4245417 | p.Gly729Arg | missense_variant | 0.4 |
embB | 4249109 | p.Pro866Thr | missense_variant | 0.77 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.73 |
ubiA | 4269296 | p.Met180Val | missense_variant | 0.29 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.71 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.71 |