Run ID: ERR10867783
Sample name:
Date: 31-03-2023 11:20:55
Number of reads: 1187064
Percentage reads mapped: 99.71
Strain: lineage4.8
Drug-resistance: MDR-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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.97 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289057 | p.Pro62Leu | 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 |
ccsA | 620135 | p.Ala82Val | missense_variant | 0.14 |
ccsA | 620204 | p.Val105Ala | missense_variant | 0.1 |
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 |
rrs | 1472870 | n.1025T>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2156283 | c.-172G>C | upstream_gene_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.22 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.22 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv1979c | 2223316 | c.-152T>C | upstream_gene_variant | 0.18 |
Rv1979c | 2223320 | c.-156T>C | upstream_gene_variant | 0.17 |
Rv1979c | 2223321 | c.-157G>A | upstream_gene_variant | 0.17 |
Rv1979c | 2223325 | c.-161G>A | upstream_gene_variant | 0.21 |
pepQ | 2859720 | p.Met233Ile | missense_variant | 0.11 |
fbiB | 3640815 | c.-720A>G | upstream_gene_variant | 0.1 |
rpoA | 3878567 | c.-60C>G | upstream_gene_variant | 0.21 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.21 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.21 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.18 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.18 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.21 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.24 |
embB | 4249735 | c.3222T>C | synonymous_variant | 0.13 |
aftB | 4268812 | p.Ser9Pro | missense_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407917 | p.Arg96Cys | missense_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |