Run ID: ERR3078008
Sample name:
Date: 01-04-2023 00:16:12
Number of reads: 872269
Percentage reads mapped: 4.86
Strain: lineage4.6.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.97 |
lineage4.6 | Euro-American | T;LAM | None | 0.97 |
lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 | 0.93 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761131 | p.Gly442Glu | missense_variant | 0.23 | rifampicin |
ahpC | 2726139 | c.-54C>T | upstream_gene_variant | 0.82 | isoniazid |
katG | 2147784 | c.-5529_*6104del | transcript_ablation | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7539 | p.Thr80Ala | missense_variant | 0.86 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.12 |
rpoB | 761126 | c.1320G>T | synonymous_variant | 0.23 |
rpoB | 761133 | p.Leu443Ile | missense_variant | 0.23 |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.21 |
rpoB | 761151 | p.Leu449Val | missense_variant | 0.21 |
rpoB | 761156 | c.1350G>C | synonymous_variant | 0.21 |
rpoB | 761159 | c.1353G>A | synonymous_variant | 0.22 |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.21 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.21 |
rpoB | 761168 | c.1362C>G | synonymous_variant | 0.21 |
rpoB | 761178 | p.Ser458Thr | missense_variant | 0.21 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.28 |
rpoB | 761196 | p.Leu464Phe | missense_variant | 0.24 |
rpoB | 761204 | c.1398C>G | synonymous_variant | 0.25 |
rpoB | 761207 | c.1401C>T | synonymous_variant | 0.29 |
rpoB | 761220 | p.Ser472Thr | missense_variant | 0.25 |
rpoB | 761234 | c.1428G>T | synonymous_variant | 0.25 |
rpoB | 761235 | p.Met477Val | missense_variant | 0.25 |
rpoB | 761252 | c.1446C>T | synonymous_variant | 0.13 |
rpoB | 761255 | c.1449T>G | synonymous_variant | 0.14 |
rpoC | 762860 | c.-510G>C | upstream_gene_variant | 0.17 |
rpoC | 762863 | c.-507T>C | upstream_gene_variant | 0.33 |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.53 |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.51 |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.51 |
rpoC | 762899 | c.-471G>C | upstream_gene_variant | 0.53 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.53 |
rpoC | 762917 | c.-453C>G | upstream_gene_variant | 0.53 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.53 |
rpoC | 762929 | c.-441G>T | upstream_gene_variant | 0.5 |
rpoB | 762930 | p.Pro1042Ser | missense_variant | 0.5 |
rpoC | 762936 | c.-434_-432delTCGinsAGC | upstream_gene_variant | 0.49 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.49 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.5 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.56 |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.54 |
rpoC | 762989 | c.-381G>T | upstream_gene_variant | 0.55 |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.42 |
rpoB | 763014 | p.Met1070Leu | missense_variant | 0.29 |
rpoB | 763017 | p.Gln1071Glu | missense_variant | 0.25 |
rpoC | 763025 | c.-345C>T | upstream_gene_variant | 0.19 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.16 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.17 |
rpoC | 763034 | c.-336C>G | upstream_gene_variant | 0.14 |
rpoC | 764902 | c.1533C>G | synonymous_variant | 0.12 |
rpoC | 764948 | c.1579T>C | synonymous_variant | 0.14 |
rpoC | 764953 | c.1584G>C | synonymous_variant | 0.14 |
rpoC | 764958 | p.Glu530Ala | missense_variant | 0.14 |
rpoC | 764968 | c.1599T>C | synonymous_variant | 0.16 |
rpoC | 766142 | c.2773C>T | synonymous_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472349 | n.504A>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472374 | n.529T>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.39 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472694 | n.849C>G | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.61 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.74 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.73 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.7 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472827 | n.982G>C | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472839 | n.994C>G | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472842 | n.997G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.93 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.93 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.9 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.84 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.81 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.79 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474875 | n.1218G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475517 | n.1860C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475518 | n.1861A>G | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475576 | n.1919C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475791 | n.2134A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476565 | n.2908G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476566 | n.2909A>G | non_coding_transcript_exon_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102116 | c.927G>T | synonymous_variant | 0.96 |
katG | 2155691 | c.421T>C | synonymous_variant | 0.29 |
katG | 2155695 | c.417C>G | synonymous_variant | 0.29 |
katG | 2155704 | c.408C>G | synonymous_variant | 0.33 |
katG | 2155716 | c.396T>G | synonymous_variant | 0.29 |
katG | 2155722 | c.390G>C | synonymous_variant | 0.33 |
katG | 2155728 | c.384G>C | synonymous_variant | 0.33 |
katG | 2155740 | p.Gly124Gln | missense_variant | 0.33 |
katG | 2155743 | c.369G>C | synonymous_variant | 0.33 |
katG | 2155782 | c.330C>G | synonymous_variant | 0.33 |
katG | 2155785 | c.327T>C | synonymous_variant | 0.33 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.21 |
ahpC | 2726507 | c.315G>T | synonymous_variant | 0.85 |
thyX | 3067814 | c.132T>C | synonymous_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4039097 | c.1608G>C | synonymous_variant | 0.13 |
clpC1 | 4039106 | c.1599G>C | synonymous_variant | 0.12 |
clpC1 | 4039112 | c.1593C>G | synonymous_variant | 0.14 |
clpC1 | 4039121 | c.1584T>C | synonymous_variant | 0.14 |
clpC1 | 4039142 | c.1563A>G | synonymous_variant | 0.14 |
clpC1 | 4039145 | c.1560G>C | synonymous_variant | 0.15 |
clpC1 | 4039169 | p.Glu512Asp | missense_variant | 0.18 |
clpC1 | 4039172 | c.1533A>G | synonymous_variant | 0.19 |
clpC1 | 4039178 | c.1527G>C | synonymous_variant | 0.2 |
clpC1 | 4039183 | c.1522T>C | synonymous_variant | 0.19 |
clpC1 | 4039186 | c.1519C>T | synonymous_variant | 0.18 |
clpC1 | 4039190 | c.1515C>G | synonymous_variant | 0.2 |
clpC1 | 4039298 | c.1407T>C | synonymous_variant | 0.12 |
clpC1 | 4039391 | c.1314T>G | synonymous_variant | 0.17 |
clpC1 | 4039409 | c.1296T>C | synonymous_variant | 0.23 |
clpC1 | 4039412 | c.1293T>G | synonymous_variant | 0.2 |
clpC1 | 4039415 | p.Glu430Asp | missense_variant | 0.19 |
clpC1 | 4039430 | c.1275T>C | synonymous_variant | 0.19 |
clpC1 | 4039442 | c.1263A>G | synonymous_variant | 0.19 |
clpC1 | 4039454 | c.1251A>G | synonymous_variant | 0.14 |
clpC1 | 4039463 | c.1242C>G | synonymous_variant | 0.12 |
clpC1 | 4039466 | c.1239T>C | synonymous_variant | 0.12 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4328329 | c.-856C>G | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.13 |