Run ID: ERR4831557
Sample name:
Date: 01-04-2023 21:00:39
Number of reads: 1794862
Percentage reads mapped: 98.81
Strain: lineage4.3.2.1;lineage4.1.1.3
Drug-resistance: Pre-XDR-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 | 0.45 |
lineage4.1 | Euro-American | T;X;H | None | 0.55 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 0.45 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.59 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 0.58 |
lineage4.3.2.1 | Euro-American (LAM) | LAM3 | RD761 | 0.43 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.55 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.63 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.68 | streptomycin |
katG | 2155167 | p.Ser315Thr | missense_variant | 0.47 | isoniazid |
pncA | 2288827 | p.Val139Met | missense_variant | 0.54 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.51 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 0.52 | ethambutol |
ethA | 4326876 | c.597delC | frameshift_variant | 0.48 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5520 | p.Pro94Leu | missense_variant | 0.47 |
gyrB | 6608 | p.Val457Leu | missense_variant | 0.54 |
gyrA | 7222 | c.-80C>T | upstream_gene_variant | 0.43 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.5 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.43 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.5 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801354 | c.546G>A | synonymous_variant | 0.51 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.47 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.98 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.48 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449616 | p.Met371Ile | missense_variant | 0.51 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3877949 | p.Thr187Ala | missense_variant | 0.52 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.45 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.51 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.27 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.57 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.37 |