Run ID: ERR2514666
Sample name:
Date: 31-03-2023 20:29:35
Number of reads: 3717248
Percentage reads mapped: 96.02
Strain: lineage4.1.1.3.1
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 | 0.99 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
lineage4.1.1.3.1 | Euro-American (X-type) | X1;X3 | RD193 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761277 | p.Ile491Phe | missense_variant | 0.86 | rifampicin |
pncA | 2288956 | p.Lys96Glu | missense_variant | 0.3 | pyrazinamide |
pncA | 2289245 | c.-5delG | upstream_gene_variant | 0.34 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.98 | ethambutol |
gid | 4408100 | c.102delG | 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 | 0.99 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 761579 | c.1773G>C | synonymous_variant | 0.13 |
rpoB | 761606 | c.1800C>G | synonymous_variant | 0.12 |
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 |
fbiC | 1303601 | p.Glu224Gly | missense_variant | 0.97 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473813 | n.156C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475206 | n.1549C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475209 | n.1552G>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154695 | p.Val473Leu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288845 | c.388_396delGTGGTCGGT | conservative_inframe_deletion | 0.19 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3877770 | c.738A>G | synonymous_variant | 0.12 |
rpoA | 3877776 | c.732T>C | synonymous_variant | 0.12 |
rpoA | 3877782 | c.726T>C | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.99 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
aftB | 4269540 | c.-704C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |