Run ID: ERR9787061
Sample name:
Date: 02-04-2023 12:58:35
Number of reads: 1545530
Percentage reads mapped: 86.63
Strain: lineage6.2.3
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage6 | West-Africa 2 | AFRI_1 | RD702 | 0.98 |
lineage6.2 | West-Africa 2 | AFRI_1 | RD702 | 0.97 |
lineage6.2.3 | West-Africa 2 | AFRI_1 | RD702 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5072 | c.-168G>T | upstream_gene_variant | 1.0 |
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.96 |
gyrB | 7121 | p.Pro628Ser | missense_variant | 0.94 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7480 | p.Phe60Tyr | missense_variant | 0.14 |
gyrA | 7547 | c.246C>T | synonymous_variant | 0.16 |
gyrA | 7562 | c.261C>T | synonymous_variant | 0.15 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7625 | c.324G>C | synonymous_variant | 0.15 |
gyrA | 7631 | c.330G>C | synonymous_variant | 0.15 |
gyrA | 7637 | c.336C>G | synonymous_variant | 0.15 |
gyrA | 8493 | p.Leu398Phe | missense_variant | 0.95 |
gyrA | 8672 | c.1371A>G | synonymous_variant | 0.16 |
gyrA | 8678 | c.1377G>A | synonymous_variant | 0.15 |
gyrA | 8693 | c.1392T>C | synonymous_variant | 0.16 |
gyrA | 8711 | c.1410A>C | synonymous_variant | 0.15 |
gyrA | 8714 | c.1413A>G | synonymous_variant | 0.15 |
gyrA | 8740 | p.Arg480His | missense_variant | 0.13 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 0.93 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 760340 | c.534G>T | synonymous_variant | 0.19 |
rpoB | 760361 | c.555T>C | synonymous_variant | 0.18 |
rpoB | 760370 | c.564C>G | synonymous_variant | 0.18 |
rpoB | 760376 | p.Asp190Glu | missense_variant | 0.18 |
rpoB | 760380 | p.Thr192Leu | missense_variant | 0.18 |
rpoB | 760406 | c.600G>C | synonymous_variant | 0.21 |
rpoB | 760412 | c.606C>G | synonymous_variant | 0.23 |
rpoB | 760424 | c.618C>G | synonymous_variant | 0.23 |
rpoB | 760430 | c.624T>C | synonymous_variant | 0.25 |
rpoB | 760475 | c.669A>G | synonymous_variant | 0.24 |
rpoB | 760481 | c.675G>C | synonymous_variant | 0.24 |
rpoB | 760484 | c.678A>G | synonymous_variant | 0.24 |
rpoB | 760522 | p.Ser239Asn | missense_variant | 0.18 |
rpoB | 760532 | c.726T>C | synonymous_variant | 0.18 |
rpoB | 760533 | p.Val243Thr | missense_variant | 0.18 |
rpoB | 760541 | c.735G>C | synonymous_variant | 0.19 |
rpoB | 760547 | c.741G>C | synonymous_variant | 0.19 |
rpoB | 760563 | p.Arg253Met | missense_variant | 0.19 |
rpoB | 760591 | p.Val262Ala | missense_variant | 0.21 |
rpoB | 760611 | c.805T>C | synonymous_variant | 0.18 |
rpoB | 760969 | p.Ser388Leu | missense_variant | 0.94 |
rpoB | 761723 | p.Glu639Asp | missense_variant | 0.92 |
rpoB | 761906 | c.2100C>G | synonymous_variant | 0.15 |
rpoB | 761916 | p.Asp704Asn | missense_variant | 0.14 |
rpoB | 762014 | c.2208C>T | synonymous_variant | 0.16 |
rpoB | 762017 | c.2211A>G | synonymous_variant | 0.16 |
rpoB | 762101 | c.2295C>G | synonymous_variant | 0.16 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.16 |
rpoC | 762995 | c.-375G>T | upstream_gene_variant | 0.19 |
rpoC | 763013 | c.-357C>G | upstream_gene_variant | 0.23 |
rpoC | 763025 | c.-345C>T | upstream_gene_variant | 0.22 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.22 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763034 | c.-336C>G | upstream_gene_variant | 0.25 |
rpoC | 763040 | c.-330C>G | upstream_gene_variant | 0.27 |
rpoC | 763070 | c.-300T>C | upstream_gene_variant | 0.29 |
rpoC | 763085 | c.-285C>G | upstream_gene_variant | 0.28 |
rpoC | 763115 | c.-255T>C | upstream_gene_variant | 0.24 |
rpoC | 763136 | c.-234C>T | upstream_gene_variant | 0.19 |
rpoC | 763148 | c.-222G>C | upstream_gene_variant | 0.18 |
rpoC | 763158 | c.-212C>T | upstream_gene_variant | 0.17 |
rpoC | 763166 | c.-204A>G | upstream_gene_variant | 0.16 |
rpoC | 763441 | c.72C>T | synonymous_variant | 0.15 |
rpoC | 763444 | c.75T>C | synonymous_variant | 0.15 |
rpoC | 763723 | c.354G>C | synonymous_variant | 0.15 |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.15 |
rpoC | 763741 | c.372C>T | synonymous_variant | 0.14 |
rpoC | 763853 | p.Val162Ile | missense_variant | 0.16 |
rpoC | 764365 | c.996C>T | synonymous_variant | 0.15 |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.16 |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.17 |
rpoC | 764815 | c.1446A>G | synonymous_variant | 0.18 |
rpoC | 764827 | c.1458G>C | synonymous_variant | 0.19 |
rpoC | 765700 | c.2331T>C | synonymous_variant | 0.16 |
rpoC | 765734 | c.2365T>C | synonymous_variant | 0.16 |
rpoC | 765739 | c.2370G>T | synonymous_variant | 0.15 |
rpoC | 765751 | c.2382C>G | synonymous_variant | 0.16 |
rpoC | 765753 | p.Asp795Ala | missense_variant | 0.16 |
rpoC | 765772 | c.2403C>G | synonymous_variant | 0.18 |
rpoC | 765787 | c.2418C>T | synonymous_variant | 0.15 |
rpoC | 765793 | c.2424C>G | synonymous_variant | 0.17 |
rpoC | 765796 | c.2427C>T | synonymous_variant | 0.16 |
rpoC | 765811 | c.2442T>C | synonymous_variant | 0.17 |
rpoC | 765814 | c.2445A>G | synonymous_variant | 0.17 |
rpoC | 765826 | c.2457T>C | synonymous_variant | 0.17 |
rpoC | 765835 | c.2466C>T | synonymous_variant | 0.17 |
rpoC | 765850 | c.2481G>C | synonymous_variant | 0.19 |
rpoC | 766135 | c.2766G>A | synonymous_variant | 0.14 |
rpoC | 766996 | c.3627C>T | synonymous_variant | 0.13 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781868 | c.309T>C | synonymous_variant | 0.15 |
rpsL | 781871 | c.312G>C | synonymous_variant | 0.15 |
rpsL | 781877 | c.318T>C | synonymous_variant | 0.15 |
rpsL | 781898 | c.339A>T | synonymous_variant | 0.15 |
rpsL | 781916 | c.357T>C | synonymous_variant | 0.15 |
rpsL | 781929 | p.Gly124Ser | missense_variant | 0.16 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
fbiC | 1303948 | p.Gly340Arg | missense_variant | 0.14 |
fbiC | 1303961 | p.Arg344Leu | missense_variant | 0.14 |
fbiC | 1303980 | c.1050G>A | synonymous_variant | 0.14 |
fbiC | 1304928 | c.1998T>C | synonymous_variant | 0.14 |
fbiC | 1304937 | c.2007G>C | synonymous_variant | 0.15 |
fbiC | 1304958 | c.2028T>G | synonymous_variant | 0.15 |
fbiC | 1304983 | c.2053C>T | synonymous_variant | 0.17 |
fbiC | 1304995 | p.Leu689Met | missense_variant | 0.14 |
Rv1258c | 1406685 | p.Val219Ala | missense_variant | 1.0 |
embR | 1416633 | p.Leu239Val | missense_variant | 1.0 |
atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1473899 | n.242A>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1473986 | n.329T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473987 | n.330G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474093 | n.436G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474904 | n.1247G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474961 | n.1304T>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474963 | n.1306G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474964 | n.1307T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474970 | n.1313G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475642 | n.1985T>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475765 | n.2111delG | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476086 | n.2429G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.15 |
inhA | 1674414 | c.213G>A | synonymous_variant | 1.0 |
inhA | 1674434 | p.Val78Ala | missense_variant | 0.98 |
rpsA | 1833787 | c.246C>G | synonymous_variant | 0.15 |
rpsA | 1833790 | c.249T>C | synonymous_variant | 0.15 |
rpsA | 1833802 | c.261A>G | synonymous_variant | 0.17 |
rpsA | 1833811 | c.270G>T | synonymous_variant | 0.15 |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.15 |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.19 |
rpsA | 1834366 | c.825A>G | synonymous_variant | 0.2 |
rpsA | 1834396 | c.855G>C | synonymous_variant | 0.21 |
rpsA | 1834411 | c.870T>C | synonymous_variant | 0.23 |
rpsA | 1834417 | c.876G>C | synonymous_variant | 0.24 |
rpsA | 1834423 | c.882G>C | synonymous_variant | 0.23 |
rpsA | 1834435 | c.894G>C | synonymous_variant | 0.22 |
rpsA | 1834451 | c.910T>C | synonymous_variant | 0.19 |
rpsA | 1834465 | c.924T>C | synonymous_variant | 0.16 |
rpsA | 1834468 | c.927A>G | synonymous_variant | 0.16 |
rpsA | 1834489 | c.948T>C | synonymous_variant | 0.16 |
rpsA | 1834775 | p.Ala412Thr | missense_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155503 | c.609C>T | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518744 | c.630C>T | synonymous_variant | 0.16 |
kasA | 2518747 | c.633C>G | synonymous_variant | 0.15 |
kasA | 2518768 | c.654C>T | synonymous_variant | 0.18 |
kasA | 2518777 | c.663C>T | synonymous_variant | 0.19 |
kasA | 2518783 | c.669T>C | synonymous_variant | 0.19 |
kasA | 2518789 | c.675G>C | synonymous_variant | 0.19 |
kasA | 2518792 | c.678C>A | synonymous_variant | 0.19 |
kasA | 2518795 | c.681C>G | synonymous_variant | 0.19 |
kasA | 2518825 | c.711T>C | synonymous_variant | 0.19 |
kasA | 2518864 | c.750G>C | synonymous_variant | 0.16 |
kasA | 2518885 | c.771T>C | synonymous_variant | 0.16 |
kasA | 2518906 | c.792A>G | synonymous_variant | 0.17 |
kasA | 2518910 | p.Leu266Met | missense_variant | 0.17 |
kasA | 2518921 | c.807T>C | synonymous_variant | 0.16 |
kasA | 2518927 | c.813C>G | synonymous_variant | 0.16 |
thyX | 3067445 | c.501C>G | synonymous_variant | 0.17 |
thyX | 3067457 | c.489C>G | synonymous_variant | 0.19 |
thyX | 3067465 | p.Ile161Val | missense_variant | 0.2 |
thyX | 3067475 | c.471A>G | synonymous_variant | 0.19 |
thyX | 3067490 | c.456C>G | synonymous_variant | 0.17 |
thyX | 3067493 | c.453A>G | synonymous_variant | 0.17 |
thyX | 3067515 | p.Ser144Thr | missense_variant | 0.17 |
thyX | 3067530 | p.Ala139Ser | missense_variant | 0.18 |
thyX | 3067545 | p.Glu134Ala | missense_variant | 0.18 |
thyX | 3067549 | p.Thr133Ala | missense_variant | 0.18 |
thyX | 3067556 | p.His130Gln | missense_variant | 0.19 |
thyX | 3067559 | c.387C>G | synonymous_variant | 0.16 |
thyX | 3067565 | p.Asp127Glu | missense_variant | 0.17 |
thyX | 3067570 | p.Ala126Pro | missense_variant | 0.17 |
thyX | 3067577 | c.369G>A | synonymous_variant | 0.17 |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474352 | p.Gly116Cys | missense_variant | 0.96 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3612800 | p.Val106Ala | missense_variant | 1.0 |
alr | 3840559 | p.Arg288Ser | missense_variant | 1.0 |
alr | 3840618 | p.Asp268Gly | missense_variant | 1.0 |
rpoA | 3877613 | p.Ile299Val | missense_variant | 0.15 |
rpoA | 3877656 | c.852T>G | synonymous_variant | 0.18 |
rpoA | 3877704 | c.804G>C | synonymous_variant | 0.15 |
rpoA | 3877743 | c.765T>C | synonymous_variant | 0.14 |
rpoA | 3877782 | c.726T>C | synonymous_variant | 0.14 |
rpoA | 3877791 | c.717C>G | synonymous_variant | 0.15 |
rpoA | 3877890 | c.618C>T | synonymous_variant | 0.14 |
rpoA | 3877896 | c.612G>C | synonymous_variant | 0.14 |
rpoA | 3877909 | p.Asn200Ser | missense_variant | 0.15 |
rpoA | 3877920 | c.588G>C | synonymous_variant | 0.15 |
rpoA | 3877923 | c.585C>T | synonymous_variant | 0.15 |
rpoA | 3877926 | c.582G>C | synonymous_variant | 0.15 |
rpoA | 3877962 | c.546G>T | synonymous_variant | 0.2 |
rpoA | 3877986 | c.522G>C | synonymous_variant | 0.2 |
rpoA | 3877989 | c.519A>G | synonymous_variant | 0.21 |
rpoA | 3878001 | c.507A>G | synonymous_variant | 0.21 |
rpoA | 3878022 | c.486T>C | synonymous_variant | 0.19 |
rpoA | 3878028 | c.480G>C | synonymous_variant | 0.17 |
rpoA | 3878031 | c.477T>C | synonymous_variant | 0.17 |
rpoA | 3878040 | c.468T>C | synonymous_variant | 0.17 |
rpoA | 3878043 | c.465G>A | synonymous_variant | 0.16 |
rpoA | 3878058 | c.450G>T | synonymous_variant | 0.14 |
rpoA | 3878094 | c.414C>G | synonymous_variant | 0.15 |
rpoA | 3878106 | c.402G>C | synonymous_variant | 0.15 |
rpoA | 3878118 | c.390T>C | synonymous_variant | 0.14 |
rpoA | 3878163 | c.345C>T | synonymous_variant | 0.14 |
rpoA | 3878232 | c.276G>C | synonymous_variant | 0.15 |
rpoA | 3878292 | c.216T>C | synonymous_variant | 0.16 |
rpoA | 3878304 | c.204G>C | synonymous_variant | 0.15 |
rpoA | 3878313 | c.195G>C | synonymous_variant | 0.15 |
rpoA | 3878322 | c.186A>G | synonymous_variant | 0.15 |
rpoA | 3878364 | c.144A>T | synonymous_variant | 0.16 |
rpoA | 3878385 | c.123C>G | synonymous_variant | 0.15 |
rpoA | 3878415 | c.93C>T | synonymous_variant | 0.16 |
rpoA | 3878424 | c.84G>C | synonymous_variant | 0.19 |
rpoA | 3878436 | c.72A>G | synonymous_variant | 0.2 |
rpoA | 3878442 | c.66G>C | synonymous_variant | 0.2 |
rpoA | 3878454 | c.54A>C | synonymous_variant | 0.18 |
rpoA | 3878472 | p.Asp12Glu | missense_variant | 0.14 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.16 |
clpC1 | 4038923 | c.1782A>G | synonymous_variant | 0.15 |
clpC1 | 4038953 | c.1752A>G | synonymous_variant | 0.16 |
clpC1 | 4038956 | c.1749T>C | synonymous_variant | 0.16 |
clpC1 | 4039064 | c.1641C>T | synonymous_variant | 0.15 |
clpC1 | 4039103 | c.1602T>C | synonymous_variant | 0.14 |
clpC1 | 4039616 | c.1089G>C | synonymous_variant | 0.15 |
clpC1 | 4039622 | c.1083C>T | synonymous_variant | 0.15 |
clpC1 | 4040021 | c.684A>C | synonymous_variant | 0.15 |
clpC1 | 4040024 | c.681A>G | synonymous_variant | 0.15 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241665 | c.1803G>C | synonymous_variant | 0.15 |
embC | 4241671 | c.1809T>C | synonymous_variant | 0.15 |
embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243541 | c.309C>T | synonymous_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 |
embB | 4246864 | c.351C>T | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4247716 | c.1203C>T | synonymous_variant | 0.14 |
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 0.96 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.98 |
aftB | 4269522 | c.-686C>T | upstream_gene_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.98 |
ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |