Run ID: ERR4799300
Sample name:
Date: 01-04-2023 09:01:12
Number of reads: 2910789
Percentage reads mapped: 99.66
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 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.98 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.98 | isoniazid |
pncA | 2288779 | p.Val155Met | missense_variant | 0.99 | pyrazinamide |
embB | 4248002 | p.Gln497Lys | missense_variant | 0.98 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5332 | c.93C>T | synonymous_variant | 0.99 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8168 | p.Glu289Asp | missense_variant | 1.0 |
rpoC | 765612 | p.His748Pro | missense_variant | 0.99 |
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 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.94 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
folC | 2747470 | p.Ile43Ala | missense_variant | 0.98 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 0.71 |
Rv3083 | 3448500 | c.-4A>G | upstream_gene_variant | 0.6 |
Rv3083 | 3448501 | c.-3G>T | upstream_gene_variant | 0.6 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245417 | p.Gly729Arg | missense_variant | 0.99 |
ubiA | 4269298 | p.Ile179Thr | missense_variant | 0.98 |
ethA | 4327301 | p.Asp58Gly | missense_variant | 0.96 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |