Run ID: SRR6045249
Sample name:
Date: 04-04-2023 11:55:33
Number of reads: 350674
Percentage reads mapped: 11.43
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 | 0.99 |
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 | 0.96 |
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 |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
pncA | 2289223 | p.Val7Leu | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6589 | c.-713G>T | upstream_gene_variant | 0.2 |
gyrB | 7166 | p.Ala643Thr | missense_variant | 0.22 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8841 | p.Glu514Lys | missense_variant | 0.29 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576076 | c.729T>C | synonymous_variant | 0.14 |
mshA | 576311 | p.Ser322Thr | missense_variant | 0.11 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 765612 | p.His748Pro | missense_variant | 0.87 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpS5 | 778851 | p.Ala19Ser | missense_variant | 0.33 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303601 | p.Glu224Gly | missense_variant | 1.0 |
atpE | 1461083 | c.39T>G | synonymous_variant | 0.22 |
atpE | 1461238 | p.Phe65Ser | missense_variant | 0.13 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471913 | n.68A>G | non_coding_transcript_exon_variant | 0.29 |
inhA | 1673931 | c.-271C>A | upstream_gene_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101884 | p.Phe387Leu | missense_variant | 0.12 |
ndh | 2102648 | p.Ala132Val | missense_variant | 0.15 |
katG | 2154695 | p.Val473Leu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2715057 | c.276C>T | synonymous_variant | 0.18 |
eis | 2715060 | p.His91Met | missense_variant | 0.2 |
eis | 2715065 | p.Thr90Ala | missense_variant | 0.2 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.33 |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.4 |
Rv2752c | 3065461 | p.Arg244Gln | missense_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086811 | c.-9G>C | upstream_gene_variant | 0.11 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3840325 | p.Phe366Leu | missense_variant | 0.14 |
alr | 3840490 | p.Pro311Ser | missense_variant | 0.2 |
clpC1 | 4039484 | c.1221T>G | synonymous_variant | 0.5 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4245076 | p.Ala615Val | missense_variant | 0.22 |
embB | 4248448 | c.1935C>A | synonymous_variant | 0.15 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
embB | 4249753 | p.Leu1080Phe | missense_variant | 0.25 |
aftB | 4269540 | c.-704C>T | upstream_gene_variant | 1.0 |
ethA | 4326899 | p.Pro192Leu | missense_variant | 0.25 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407751 | p.Pro151Gln | missense_variant | 0.12 |