Run ID: ERR025841
Sample name:
Date: 31-03-2023 08:18:06
Number of reads: 457107
Percentage reads mapped: 99.05
Strain: lineage4.1.2.1
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1.2 | Euro-American | T;H | None | 0.21 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.11 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.33 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.33 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5520 | p.Pro94Leu | missense_variant | 0.23 |
gyrB | 7121 | p.Pro628Ala | missense_variant | 0.36 |
gyrA | 7222 | c.-80C>T | upstream_gene_variant | 0.33 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9293 | c.1992G>T | synonymous_variant | 0.25 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490696 | c.-87T>G | upstream_gene_variant | 0.25 |
mshA | 576077 | c.730C>T | synonymous_variant | 0.2 |
rpoB | 759831 | p.Thr9Pro | missense_variant | 0.23 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.22 |
rpoC | 764725 | p.Phe452Leu | missense_variant | 0.5 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.27 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406750 | c.591C>A | synonymous_variant | 0.2 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.38 |
inhA | 1674892 | p.Asn231Asp | missense_variant | 0.4 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168366 | c.2247G>A | synonymous_variant | 0.18 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.12 |
Rv1979c | 2222982 | c.183G>T | synonymous_variant | 0.21 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.38 |
pepQ | 2860260 | c.159G>A | synonymous_variant | 0.36 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.5 |
Rv2752c | 3067012 | c.-821C>G | upstream_gene_variant | 0.29 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.5 |
thyA | 3074654 | c.-183T>G | upstream_gene_variant | 0.25 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.57 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475348 | p.Ala448Thr | missense_variant | 0.25 |
clpC1 | 4038319 | p.Pro796Ala | missense_variant | 0.62 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.25 |
embC | 4242482 | p.Asn874His | missense_variant | 0.67 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.4 |
embC | 4242806 | p.Phe982Ile | missense_variant | 0.4 |
embC | 4243045 | p.Gln1061His | missense_variant | 0.4 |
embA | 4243624 | p.Ile131Ser | missense_variant | 0.33 |
embB | 4246845 | p.Leu111Ser | missense_variant | 0.18 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.29 |
ethA | 4326996 | p.Pro160Thr | missense_variant | 0.43 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.33 |