Run ID: ERR2706966
Sample name:
Date: 31-03-2023 23:11:45
Number of reads: 4019803
Percentage reads mapped: 99.58
Strain: lineage4.6.1.2;lineage4.3.3
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.44 |
lineage4.6 | Euro-American | T;LAM | None | 0.59 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.43 |
lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 | 0.55 |
lineage4.6.1.2 | Euro-American | T2 | RD724 | 0.57 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Trp | missense_variant | 0.12 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.15 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.14 | isoniazid |
pncA | 2289091 | p.His51Tyr | missense_variant | 0.2 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5723 | p.Ala162Ser | missense_variant | 0.32 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7539 | p.Thr80Ala | missense_variant | 0.72 |
gyrA | 7570 | p.Ala90Gly | missense_variant | 0.69 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.47 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 575240 | c.-108G>A | upstream_gene_variant | 0.22 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.17 |
rpoC | 764810 | p.Pro481Thr | missense_variant | 0.42 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.45 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpS5 | 779675 | c.-770G>A | upstream_gene_variant | 0.16 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304608 | p.Thr560Ala | missense_variant | 0.17 |
embR | 1416410 | p.Leu313Arg | missense_variant | 0.55 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475373 | n.1716G>A | non_coding_transcript_exon_variant | 0.63 |
fabG1 | 1673277 | c.-163_-162insT | upstream_gene_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.46 |
eis | 2715432 | c.-100C>T | upstream_gene_variant | 0.13 |
ribD | 2987533 | p.Gly232Ala | missense_variant | 0.15 |
Rv2752c | 3065920 | p.Pro91Leu | missense_variant | 0.57 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.28 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.4 |
Rv3083 | 3449301 | c.798G>A | synonymous_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
ddn | 3987215 | c.372A>G | synonymous_variant | 0.58 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.45 |
embC | 4242182 | p.Ala774Ser | missense_variant | 0.28 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245055 | p.Thr608Asn | missense_variant | 0.65 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.24 |
embB | 4247209 | c.696A>G | synonymous_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407926 | p.Pro93Ser | missense_variant | 0.16 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.37 |