Run ID: ERR4821179
Sample name:
Date: 20-10-2023 09:33:56
Number of reads: 3409122
Percentage reads mapped: 89.99
Strain: lineage4.1.2.1
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | R | rrs n.888G>A (0.86) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
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 | 0.99 |
lineage4.1.2 | Euro-American | T;H | None | 1.0 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.86 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7216 | c.-86G>C | upstream_gene_variant | 0.12 |
gyrA | 7225 | c.-77T>C | upstream_gene_variant | 0.12 |
gyrA | 7237 | c.-65C>T | upstream_gene_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7715 | c.414G>C | synonymous_variant | 0.12 |
gyrA | 8603 | c.1302A>G | synonymous_variant | 0.17 |
gyrA | 8619 | c.1318T>C | synonymous_variant | 0.17 |
gyrA | 8624 | c.1323G>C | synonymous_variant | 0.18 |
gyrA | 8627 | c.1326C>G | synonymous_variant | 0.18 |
gyrA | 8636 | c.1335A>C | synonymous_variant | 0.13 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 |
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.92 |
rpoB | 761531 | c.1725C>G | synonymous_variant | 0.12 |
rpoB | 761537 | c.1731C>G | synonymous_variant | 0.12 |
rpoB | 761570 | c.1764T>C | synonymous_variant | 0.12 |
rpoB | 762254 | c.2448T>C | synonymous_variant | 0.14 |
rpoB | 762266 | c.2460T>C | synonymous_variant | 0.13 |
rpoB | 762284 | c.2478G>C | synonymous_variant | 0.16 |
rpoB | 762293 | c.2487T>C | synonymous_variant | 0.16 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.13 |
rpoC | 762995 | c.-375G>T | upstream_gene_variant | 0.15 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.25 |
rpoC | 763031 | c.-339T>G | upstream_gene_variant | 0.24 |
rpoC | 763034 | c.-336C>G | upstream_gene_variant | 0.24 |
rpoC | 763040 | c.-330C>G | upstream_gene_variant | 0.21 |
rpoC | 763070 | c.-300T>C | upstream_gene_variant | 0.16 |
rpoC | 763076 | c.-294C>G | upstream_gene_variant | 0.15 |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.12 |
rpoC | 763723 | c.354G>C | synonymous_variant | 0.14 |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.15 |
rpoC | 763735 | c.366G>C | synonymous_variant | 0.14 |
rpoC | 763744 | c.375G>C | synonymous_variant | 0.13 |
rpoC | 763996 | c.627T>C | synonymous_variant | 0.17 |
rpoC | 764005 | c.636G>C | synonymous_variant | 0.17 |
rpoC | 764011 | c.642T>C | synonymous_variant | 0.17 |
rpoC | 764040 | p.Ser224Asn | missense_variant | 0.14 |
rpoC | 764044 | c.675T>C | synonymous_variant | 0.14 |
rpoC | 764116 | c.747C>T | synonymous_variant | 0.12 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.12 |
rpoC | 764824 | c.1455T>C | synonymous_variant | 0.12 |
rpoC | 764830 | c.1461C>G | synonymous_variant | 0.13 |
rpoC | 764872 | c.1503A>G | synonymous_variant | 0.12 |
rpoC | 764893 | c.1524T>C | synonymous_variant | 0.13 |
rpoC | 764911 | c.1542A>G | synonymous_variant | 0.13 |
rpoC | 764932 | c.1563C>A | synonymous_variant | 0.12 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766864 | c.3495G>C | synonymous_variant | 0.13 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304808 | c.1878C>G | synonymous_variant | 0.13 |
fbiC | 1304811 | c.1881C>G | synonymous_variant | 0.14 |
fbiC | 1304817 | c.1887T>C | synonymous_variant | 0.16 |
fbiC | 1304829 | c.1899T>C | synonymous_variant | 0.25 |
fbiC | 1304832 | c.1902C>G | synonymous_variant | 0.23 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.98 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.98 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.66 |
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.74 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.73 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.73 |
rrs | 1472670 | n.825G>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.85 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.84 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.87 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.87 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.9 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.86 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.34 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.75 |
inhA | 1674537 | c.336C>G | synonymous_variant | 0.17 |
inhA | 1674542 | p.Ala114Glu | missense_variant | 0.16 |
inhA | 1674549 | c.348G>C | synonymous_variant | 0.13 |
inhA | 1674561 | c.360C>T | synonymous_variant | 0.14 |
inhA | 1674582 | c.381T>C | synonymous_variant | 0.18 |
inhA | 1674585 | c.384T>C | synonymous_variant | 0.19 |
inhA | 1674589 | p.Met130Leu | missense_variant | 0.19 |
inhA | 1674624 | c.423A>C | synonymous_variant | 0.13 |
inhA | 1674627 | c.426T>C | synonymous_variant | 0.13 |
inhA | 1674630 | c.429C>G | synonymous_variant | 0.13 |
inhA | 1674636 | c.435C>G | synonymous_variant | 0.14 |
inhA | 1674654 | c.453G>C | synonymous_variant | 0.14 |
rpsA | 1833554 | p.Thr5Ala | missense_variant | 0.18 |
rpsA | 1833568 | c.27G>C | synonymous_variant | 0.2 |
rpsA | 1833589 | c.48A>T | synonymous_variant | 0.17 |
rpsA | 1833595 | c.54T>C | synonymous_variant | 0.18 |
rpsA | 1833619 | c.78A>C | synonymous_variant | 0.17 |
rpsA | 1833724 | c.183C>G | synonymous_variant | 0.15 |
rpsA | 1833742 | c.201A>G | synonymous_variant | 0.14 |
rpsA | 1833745 | c.204G>C | synonymous_variant | 0.17 |
rpsA | 1833787 | c.246C>G | synonymous_variant | 0.16 |
rpsA | 1833790 | c.249T>A | synonymous_variant | 0.16 |
rpsA | 1833799 | c.258C>G | synonymous_variant | 0.15 |
rpsA | 1833811 | c.270G>C | synonymous_variant | 0.17 |
rpsA | 1833838 | c.297G>C | synonymous_variant | 0.21 |
rpsA | 1833841 | c.300C>G | synonymous_variant | 0.21 |
rpsA | 1833847 | c.306C>G | synonymous_variant | 0.21 |
rpsA | 1833856 | c.315A>G | synonymous_variant | 0.25 |
rpsA | 1833862 | c.321G>T | synonymous_variant | 0.24 |
rpsA | 1833874 | c.333T>C | synonymous_variant | 0.31 |
rpsA | 1833928 | c.387G>C | synonymous_variant | 0.17 |
rpsA | 1833940 | c.399C>G | synonymous_variant | 0.14 |
rpsA | 1834261 | c.720A>C | synonymous_variant | 0.13 |
rpsA | 1834264 | c.723G>C | synonymous_variant | 0.13 |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.12 |
rpsA | 1834451 | c.910T>C | synonymous_variant | 0.14 |
rpsA | 1834498 | c.957C>T | synonymous_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2155032 | c.1080T>C | synonymous_variant | 0.13 |
katG | 2155054 | p.Tyr353Phe | missense_variant | 0.15 |
katG | 2155056 | c.1056A>G | synonymous_variant | 0.15 |
katG | 2155062 | c.1050T>C | synonymous_variant | 0.16 |
katG | 2155065 | c.1047C>G | synonymous_variant | 0.17 |
katG | 2155068 | c.1044T>C | synonymous_variant | 0.16 |
katG | 2155071 | c.1041T>C | synonymous_variant | 0.16 |
katG | 2155080 | c.1032G>C | synonymous_variant | 0.17 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
thyA | 3073953 | c.519T>C | synonymous_variant | 0.14 |
thyA | 3073977 | c.495A>G | synonymous_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3877587 | c.921A>G | synonymous_variant | 0.14 |
rpoA | 3878143 | p.Gly122Asp | missense_variant | 0.11 |
clpC1 | 4038530 | p.Glu725Asp | missense_variant | 0.13 |
clpC1 | 4038536 | c.2169C>T | synonymous_variant | 0.12 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.16 |
clpC1 | 4038908 | c.1797C>G | synonymous_variant | 0.2 |
clpC1 | 4038914 | c.1791G>C | synonymous_variant | 0.21 |
clpC1 | 4039178 | c.1527G>C | synonymous_variant | 0.13 |
clpC1 | 4039187 | c.1518G>C | synonymous_variant | 0.12 |
clpC1 | 4039190 | c.1515C>G | synonymous_variant | 0.12 |
clpC1 | 4039208 | c.1497C>G | synonymous_variant | 0.16 |
clpC1 | 4039226 | c.1479T>C | synonymous_variant | 0.25 |
clpC1 | 4039268 | c.1437C>G | synonymous_variant | 0.29 |
clpC1 | 4039274 | c.1431G>C | synonymous_variant | 0.25 |
clpC1 | 4039286 | c.1419T>C | synonymous_variant | 0.18 |
clpC1 | 4039289 | c.1416T>C | synonymous_variant | 0.18 |
clpC1 | 4039295 | c.1410A>C | synonymous_variant | 0.2 |
clpC1 | 4039298 | c.1407T>C | synonymous_variant | 0.22 |
clpC1 | 4039319 | c.1386T>C | synonymous_variant | 0.17 |
clpC1 | 4039322 | c.1383T>C | synonymous_variant | 0.15 |
clpC1 | 4039493 | c.1212C>T | synonymous_variant | 0.17 |
clpC1 | 4039517 | c.1188C>G | synonymous_variant | 0.17 |
clpC1 | 4039524 | p.Phe394Tyr | missense_variant | 0.17 |
clpC1 | 4039526 | c.1179G>C | synonymous_variant | 0.15 |
clpC1 | 4039532 | c.1173C>T | synonymous_variant | 0.15 |
clpC1 | 4039586 | c.1119G>C | synonymous_variant | 0.15 |
clpC1 | 4039898 | c.807C>G | synonymous_variant | 0.2 |
clpC1 | 4039904 | c.801A>G | synonymous_variant | 0.22 |
clpC1 | 4039928 | c.775_777delAGCinsTCG | synonymous_variant | 0.21 |
clpC1 | 4039931 | c.774T>C | synonymous_variant | 0.18 |
clpC1 | 4039946 | c.759A>T | synonymous_variant | 0.18 |
clpC1 | 4039952 | c.753T>C | synonymous_variant | 0.18 |
clpC1 | 4039958 | c.747G>C | synonymous_variant | 0.15 |
clpC1 | 4039979 | c.726C>G | synonymous_variant | 0.13 |
clpC1 | 4040465 | c.240T>C | synonymous_variant | 0.14 |
clpC1 | 4040471 | c.234T>C | synonymous_variant | 0.18 |
clpC1 | 4040477 | c.228G>A | synonymous_variant | 0.18 |
clpC1 | 4040480 | c.225T>C | synonymous_variant | 0.19 |
clpC1 | 4040522 | c.183T>C | synonymous_variant | 0.12 |
embC | 4240561 | c.699C>G | synonymous_variant | 0.12 |
embC | 4240578 | p.Ala239Val | missense_variant | 0.13 |
embC | 4240582 | c.720C>G | synonymous_variant | 0.13 |
embC | 4240591 | c.729C>G | synonymous_variant | 0.13 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.98 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |