Run ID: ERR2516663
Sample name:
Date: 31-03-2023 21:39:59
Number of reads: 1866918
Percentage reads mapped: 99.62
Strain: lineage4.1.1.3
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 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.23 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764948 | p.Leu527Val | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289199 | p.Glu15* | stop_gained | 1.0 | pyrazinamide |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol |
ethA | 4327159 | c.314dupT | frameshift_variant | 1.0 | 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 | 8164 | p.Ala288Asp | missense_variant | 0.75 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776813 | c.1668G>A | synonymous_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302954 | c.24G>A | synonymous_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471861 | n.16T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1471872 | n.27T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1471947 | n.102G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472363 | n.518G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1473279 | n.1434G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476785 | n.3128A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476795 | n.3138A>G | splice_region_variant&non_coding_transcript_exon_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154678 | c.1434G>C | synonymous_variant | 1.0 |
PPE35 | 2169405 | p.Asn403Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726409 | p.Asp73His | missense_variant | 1.0 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449437 | c.936_942delCGCGGCG | frameshift_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.13 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.98 |
embB | 4249678 | c.3165C>A | synonymous_variant | 1.0 |
ubiA | 4269296 | p.Met180Val | missense_variant | 1.0 |
gid | 4407934 | p.Leu90Arg | missense_variant | 1.0 |
whiB6 | 4337479 | c.-219_*691del | transcript_ablation | 1.0 |