Run ID: ERR2653117
Sample name:
Date: 31-03-2023 22:32:16
Number of reads: 907862
Percentage reads mapped: 99.25
Strain: lineage4.3.4.2
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.99 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.17 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288797 | c.443_444dupGC | frameshift_variant | 0.98 | pyrazinamide |
folC | 2747480 | p.Glu40Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
alr | 3840393 | p.Met343Thr | missense_variant | 0.98 | cycloserine |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.96 | ethambutol |
ethA | 4326622 | c.851dupC | frameshift_variant | 0.96 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 0.95 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.82 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1305494 | c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT | frameshift_variant&stop_lost&splice_region_variant | 0.25 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474428 | n.771C>T | non_coding_transcript_exon_variant | 0.11 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2167797 | p.Leu939Pro | missense_variant | 0.85 |
PPE35 | 2169744 | p.Ala290Glu | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.13 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
alr | 3840719 | c.702A>G | synonymous_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243225 | c.-8C>T | upstream_gene_variant | 0.28 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407991 | p.Gly71Val | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
fbiC | 1305494 | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | frameshift_variant&stop_lost&splice_region_variant | 1.0 |