Run ID: ERR10610078
Sample name:
Date: 19-05-2023 07:49:59
Number of reads: 839050
Percentage reads mapped: 98.92
Strain: lineage4.1.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Val (0.18), rpoB p.Ser450Leu (0.88) |
Isoniazid | R | katG p.Ser315Thr (1.00), ahpC c.-57C>T (0.95) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Thr135Pro (0.95) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.860delA (0.95), ethA c.860delA (0.95) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1 | Euro-American | T;X;H | None | 0.99 |
lineage4.1.2 | Euro-American | T;H | None | 0.96 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.97 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761110 | p.Asp435Val | missense_variant | 0.18 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.88 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288839 | p.Thr135Pro | missense_variant | 0.95 | pyrazinamide |
ahpC | 2726136 | c.-57C>T | upstream_gene_variant | 0.95 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4326613 | c.860delA | frameshift_variant | 0.95 | ethionamide, 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491382 | p.Glu200Asp | missense_variant | 0.38 |
fgd1 | 491386 | p.Leu202Ile | missense_variant | 0.29 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.17 |
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474823 | n.1166C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
kasA | 2519214 | p.Ile367Ser | missense_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3878049 | c.459G>C | synonymous_variant | 0.2 |
clpC1 | 4038444 | p.Ala754Val | missense_variant | 0.12 |
clpC1 | 4038662 | c.2043T>C | synonymous_variant | 0.14 |
clpC1 | 4039064 | c.1641C>T | synonymous_variant | 0.15 |
clpC1 | 4039094 | c.1611C>G | synonymous_variant | 0.14 |
clpC1 | 4039097 | c.1608G>C | synonymous_variant | 0.13 |
clpC1 | 4039103 | c.1602T>C | synonymous_variant | 0.15 |
clpC1 | 4039106 | c.1599G>C | synonymous_variant | 0.14 |
clpC1 | 4039112 | c.1593C>G | synonymous_variant | 0.13 |
clpC1 | 4039121 | c.1584T>C | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338635 | c.-114A>C | upstream_gene_variant | 1.0 |
whiB6 | 4338699 | c.-179delT | upstream_gene_variant | 0.14 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.11 |