Run ID: ERR1034662
Sample name:
Date: 31-03-2023 09:32:28
Number of reads: 3587195
Percentage reads mapped: 99.53
Strain: lineage4.1.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
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 | 1.0 |
lineage4.1.2 | Euro-American | T;H | None | 1.0 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin |
rpoB | 761110 | p.Asp435Gly | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
pncA | 2289039 | p.Trp68Ser | missense_variant | 0.98 | pyrazinamide |
folC | 2747471 | p.Ile43Thr | missense_variant | 0.64 | para-aminosalicylic_acid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
gid | 4408125 | c.77delT | frameshift_variant | 1.0 | streptomycin |
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 | 491591 | p.Lys270Met | missense_variant | 1.0 |
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 |
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 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.21 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.22 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
folC | 2746880 | p.Lys240Thr | missense_variant | 0.57 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.21 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.43 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3878641 | c.-135delG | upstream_gene_variant | 0.12 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.22 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4249397 | p.Ala962Pro | missense_variant | 0.17 |
ethA | 4326276 | p.Glu400Lys | missense_variant | 0.59 |
ethA | 4326284 | p.Leu397Pro | missense_variant | 0.17 |
ethA | 4326362 | p.Gly371Val | missense_variant | 0.27 |
whiB6 | 4336748 | c.-400_*1422del | transcript_ablation | 1.0 |