Run ID: SRR25827450
Sample name:
Date: 15-03-2024 13:50:21
Number of reads: 7495709
Percentage reads mapped: 98.88
Strain: lineage4.1.1.1;lineage3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.58) |
Isoniazid | R | katG p.Ser315Thr (0.42) |
Ethambutol | ||
Pyrazinamide | R | pncA p.Thr142Met (0.43) |
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.51 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.51 |
lineage4.1 | Euro-American | T;X;H | None | 0.48 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.47 |
lineage4.1.1.1 | Euro-American (X-type) | X2 | RD183 | 0.45 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.58 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.42 | isoniazid |
pncA | 2288817 | p.Thr142Met | missense_variant | 0.43 | pyrazinamide |
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 | 0.59 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.5 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.53 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.56 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.49 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.52 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476436 | n.2779A>G | non_coding_transcript_exon_variant | 0.46 |
inhA | 1673368 | c.-834A>G | upstream_gene_variant | 0.43 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.49 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.48 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.53 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.5 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.52 |
ahpC | 2726210 | c.18T>C | synonymous_variant | 0.47 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fbiA | 3641447 | p.Thr302Met | missense_variant | 0.5 |
rpoA | 3877553 | p.Glu319Lys | missense_variant | 0.44 |
embC | 4240897 | c.1035C>G | synonymous_variant | 0.53 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.57 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.43 |
embA | 4245835 | p.Leu868Arg | missense_variant | 0.18 |
embB | 4247015 | p.Ser168Ala | missense_variant | 0.23 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.42 |
aftB | 4269096 | c.-260C>G | upstream_gene_variant | 0.45 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.55 |