Run ID: ERR1034911
Sample name:
Date: 31-03-2023 09:49:28
Number of reads: 6581217
Percentage reads mapped: 99.01
Strain: lineage4.3.4.2;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 | 1.0 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.49 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.51 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.52 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761100 | p.Gln432Glu | missense_variant | 0.57 | rifampicin |
rpoB | 761110 | p.Asp435Val | missense_variant | 0.56 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.49 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.45 | isoniazid, ethionamide |
inhA | 1674782 | p.Ile194Thr | missense_variant | 0.56 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.52 | isoniazid |
pncA | 2288852 | c.389_390insA | frameshift_variant | 0.42 | pyrazinamide, pyrazinamide |
pncA | 2288868 | p.Val125Gly | missense_variant | 0.56 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.44 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 0.51 | ethambutol |
embB | 4247781 | p.Met423Thr | missense_variant | 0.48 | ethambutol |
gid | 4407965 | p.Ala80Pro | missense_variant | 0.54 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 0.53 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.51 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490655 | c.-128T>C | upstream_gene_variant | 0.47 |
mshA | 576160 | c.813C>T | synonymous_variant | 0.5 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.18 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800990 | p.Lys61Thr | missense_variant | 0.37 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474632 | n.975G>T | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.1 |
rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 0.1 |
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475429 | n.1772G>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475446 | n.1789G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476214 | n.2557G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476299 | n.2642C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476583 | n.2926G>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476629 | n.2972C>A | non_coding_transcript_exon_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289743 | c.-502A>G | upstream_gene_variant | 0.17 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.48 |
thyX | 3067954 | c.-9G>A | upstream_gene_variant | 0.5 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.33 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.45 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.52 |
rpoA | 3877586 | p.Leu308Phe | missense_variant | 0.47 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embC | 4242182 | p.Ala774Ser | missense_variant | 0.44 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4328127 | c.-654C>G | upstream_gene_variant | 0.53 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408027 | p.Leu59Arg | missense_variant | 0.52 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |