Run ID: ERR4553510
Sample name:
Date: 01-04-2023 06:12:01
Number of reads: 1493398
Percentage reads mapped: 99.67
Strain: lineage4
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.75 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 0.18 |
lineage1.1.3.3 | Indo-Oceanic | NA | RD239 | 0.19 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.68 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.68 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289186 | p.Leu19Arg | missense_variant | 0.66 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.5 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6061 | p.Ser274Arg | missense_variant | 0.75 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.34 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.28 |
rpoB | 759628 | c.-179C>T | upstream_gene_variant | 0.7 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.25 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 0.12 |
rpoC | 767123 | p.Val1252Leu | missense_variant | 0.33 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.3 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407255 | p.Ala29Glu | missense_variant | 0.67 |
embR | 1416468 | p.Asp294Asn | missense_variant | 0.24 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473293 | n.1448G>C | non_coding_transcript_exon_variant | 0.52 |
rrl | 1475049 | n.1392C>T | non_coding_transcript_exon_variant | 0.18 |
inhA | 1673393 | c.-809G>A | upstream_gene_variant | 0.73 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.33 |
katG | 2156146 | c.-35A>G | upstream_gene_variant | 0.21 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.14 |
PPE35 | 2169779 | c.834A>C | synonymous_variant | 0.67 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288772 | p.Val157Gly | missense_variant | 0.29 |
pncA | 2289256 | c.-15A>C | upstream_gene_variant | 0.57 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.14 |
folC | 2746365 | c.1234C>T | synonymous_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.3 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.26 |
fprA | 3474299 | p.Asp98Gly | missense_variant | 0.67 |
Rv3236c | 3613279 | c.-163C>A | upstream_gene_variant | 0.13 |
panD | 4043957 | p.Asp109Asn | missense_variant | 0.72 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.27 |
embC | 4241736 | p.Val625Ala | missense_variant | 0.16 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 0.2 |
embB | 4247351 | p.Asp280Tyr | missense_variant | 0.2 |
embB | 4248516 | p.Val668Ala | missense_variant | 0.11 |
aftB | 4266975 | p.Pro621Arg | missense_variant | 0.19 |
ethA | 4328317 | c.-844C>T | upstream_gene_variant | 0.69 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.2 |
gid | 4407780 | c.423G>A | synonymous_variant | 0.11 |