Run ID: ERR2510724
Sample name:
Date: 31-03-2023 18:54:41
Number of reads: 2365224
Percentage reads mapped: 99.74
Strain: lineage4.8
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 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.96 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289202 | p.Cys14Gly | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304849 | p.Asn640Ser | missense_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.33 |
tlyA | 1917846 | c.-94C>A | upstream_gene_variant | 0.11 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918222 | p.Gly95Arg | missense_variant | 0.1 |
ndh | 2102074 | p.Met323Lys | missense_variant | 0.11 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.32 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.3 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518606 | c.492G>C | synonymous_variant | 0.12 |
kasA | 2518609 | p.Met165Ile | missense_variant | 0.12 |
fprA | 3474914 | p.Ala303Val | missense_variant | 0.13 |
fprA | 3474941 | p.Glu312Gly | missense_variant | 0.11 |
fbiB | 3640974 | c.-561T>G | upstream_gene_variant | 1.0 |
fbiB | 3642192 | p.Phe220Ile | missense_variant | 0.11 |
embC | 4241699 | p.Met613Val | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.11 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.1 |
embB | 4249010 | c.2497C>T | synonymous_variant | 0.1 |
ethA | 4327378 | p.Tyr32* | stop_gained | 1.0 |
whiB6 | 4338234 | c.288A>G | synonymous_variant | 1.0 |
whiB6 | 4338289 | p.Gly78Val | missense_variant | 0.17 |
whiB6 | 4338320 | p.Glu68Lys | missense_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |