Run ID: ERR046790
Sample name:
Date: 31-03-2023 08:51:13
Number of reads: 5357593
Percentage reads mapped: 97.81
Strain: lineage4.1.1.3.1
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 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
lineage4.1.1.3.1 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761277 | p.Ile491Phe | missense_variant | 1.0 | rifampicin |
katG | 2154695 | p.Val473Phe | missense_variant | 0.78 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8377 | p.Asp359Gly | missense_variant | 0.17 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490696 | c.-87T>G | upstream_gene_variant | 0.21 |
fgd1 | 491315 | p.Gly178Ala | missense_variant | 0.23 |
mshA | 576620 | p.Ala425Pro | missense_variant | 0.2 |
mshA | 576751 | p.Lys468Asn | missense_variant | 0.2 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.37 |
rpoC | 764725 | p.Phe452Leu | missense_variant | 0.24 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777399 | p.Thr361Arg | missense_variant | 0.16 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800997 | p.Asn63Lys | missense_variant | 0.18 |
fbiC | 1303601 | p.Glu224Gly | missense_variant | 0.99 |
embR | 1417136 | p.Ser71Ile | missense_variant | 0.15 |
atpE | 1461019 | c.-26C>A | upstream_gene_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475363 | n.1706C>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476408 | n.2751G>C | non_coding_transcript_exon_variant | 0.14 |
inhA | 1674892 | p.Asn231Asp | missense_variant | 0.23 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102540 | p.Ala168Gly | missense_variant | 0.22 |
ndh | 2102891 | p.Phe51Ser | missense_variant | 0.22 |
katG | 2156110 | p.Val1Gly | missense_variant | 0.26 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.37 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714366 | p.Val323Leu | missense_variant | 0.21 |
eis | 2715586 | c.-254G>C | upstream_gene_variant | 0.3 |
folC | 2746186 | c.1413G>C | synonymous_variant | 0.23 |
pepQ | 2859381 | c.1038C>G | synonymous_variant | 0.23 |
Rv2752c | 3064552 | p.Arg547Pro | missense_variant | 0.21 |
Rv2752c | 3064741 | p.Gly484Ala | missense_variant | 0.26 |
thyX | 3067995 | c.-50A>C | upstream_gene_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fbiB | 3642734 | c.1200G>C | synonymous_variant | 0.17 |
alr | 3840268 | p.Thr385Pro | missense_variant | 0.22 |
ddn | 3987013 | p.Gly57Ala | missense_variant | 0.26 |
clpC1 | 4039363 | p.Ala448Pro | missense_variant | 0.18 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.25 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.13 |
embC | 4241056 | c.1194C>G | synonymous_variant | 0.22 |
embC | 4241456 | p.Ala532Pro | missense_variant | 0.28 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4248725 | p.Ser738Ala | missense_variant | 0.32 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.13 |
aftB | 4269540 | c.-704C>T | upstream_gene_variant | 1.0 |
ethA | 4327672 | c.-199G>A | upstream_gene_variant | 0.23 |
ethR | 4327912 | p.Arg122Gly | missense_variant | 0.19 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |