Run ID: ERR7911699
Sample name:
Date: 19-10-2023 13:33:23
Number of reads: 2760590
Percentage reads mapped: 99.66
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Met175Val (1.00) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | R | gyrB p.Asp461Asn (1.00), gyrB p.Ala504Val (0.17), gyrA p.Ala90Val (0.51), gyrA p.Ser91Pro (0.21) |
Moxifloxacin | R | gyrB p.Asp461Asn (1.00), gyrB p.Ala504Val (0.17), gyrA p.Ala90Val (0.51), gyrA p.Ser91Pro (0.21) |
Ofloxacin | R | gyrB p.Asp461Asn (1.00), gyrB p.Ala504Val (0.17), gyrA p.Ala90Val (0.51), gyrA p.Ser91Pro (0.21) |
Levofloxacin | R | gyrB p.Asp461Asn (1.00), gyrB p.Ala504Val (0.17), gyrA p.Ala90Val (0.51), gyrA p.Ser91Pro (0.21) |
Ciprofloxacin | R | gyrB p.Asp461Asn (1.00), gyrB p.Ala504Val (0.17), gyrA p.Ala90Val (0.51), gyrA p.Ser91Pro (0.21) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | R | tlyA c.139_140insA (0.42) |
Kanamycin | R | eis c.-12C>T (1.00) |
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
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 |
---|---|---|---|---|---|
gyrB | 6620 | p.Asp461Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrB | 6750 | p.Ala504Val | missense_variant | 0.17 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7570 | p.Ala90Val | missense_variant | 0.51 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.21 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
tlyA | 1918078 | c.139_140insA | frameshift_variant | 0.42 | capreomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288719 | p.Met175Val | missense_variant | 1.0 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5077 | c.-163_-162insC | upstream_gene_variant | 0.13 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoC | 765862 | p.Phe831Leu | missense_variant | 1.0 |
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 | 1.0 |
PPE35 | 2169149 | c.1464G>C | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288949 | p.Ala98Val | missense_variant | 1.0 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |
ethA | 4326539 | c.866_934delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT | disruptive_inframe_deletion | 1.0 |