Run ID: ERR2027233
Sample name:
Date: 31-03-2023 15:40:34
Number of reads: 2807790
Percentage reads mapped: 56.34
Strain: lineage4.1.2.1
Drug-resistance: RR-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 | 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 |
---|---|---|---|---|---|
rpoB | 761085 | p.Thr427Ser | missense_variant | 0.5 | rifampicin |
rpoB | 761131 | p.Gly442Glu | missense_variant | 0.5 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 |
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.24 |
mshA | 576597 | p.Met417Lys | missense_variant | 0.33 |
mshA | 576701 | p.Arg452Ser | missense_variant | 0.13 |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
rpoB | 761088 | c.1282_1284delAGCinsTCG | synonymous_variant | 0.5 |
rpoB | 761097 | c.1291_1293delAGCinsTCG | synonymous_variant | 0.5 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.5 |
rpoB | 761133 | p.Leu443Val | missense_variant | 0.5 |
rpoB | 762173 | c.2367G>A | synonymous_variant | 0.18 |
rpoB | 762176 | c.2370T>G | synonymous_variant | 0.23 |
rpoB | 762181 | p.Asp792Ala | missense_variant | 0.25 |
rpoB | 762185 | c.2379G>C | synonymous_variant | 0.24 |
rpoB | 762218 | c.2412T>C | synonymous_variant | 0.35 |
rpoB | 762221 | c.2415G>A | synonymous_variant | 0.35 |
rpoB | 762223 | p.Thr806Ser | missense_variant | 0.32 |
rpoB | 762225 | p.Glu807Gln | missense_variant | 0.32 |
rpoB | 762233 | c.2427G>C | synonymous_variant | 0.29 |
rpoB | 762239 | c.2433G>A | synonymous_variant | 0.29 |
rpoB | 762243 | p.Arg813Lys | missense_variant | 0.3 |
rpoB | 762254 | c.2448T>C | synonymous_variant | 0.23 |
rpoB | 762257 | c.2451C>G | synonymous_variant | 0.22 |
rpoB | 762266 | c.2460T>C | synonymous_variant | 0.21 |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.14 |
rpoC | 762899 | c.-471G>C | upstream_gene_variant | 0.17 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.33 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.38 |
rpoC | 762923 | c.-447C>G | upstream_gene_variant | 0.39 |
rpoC | 762929 | c.-441G>T | upstream_gene_variant | 0.39 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.4 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.4 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.42 |
rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.28 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.17 |
rpoC | 764557 | p.Asn396Lys | missense_variant | 0.62 |
rpoC | 764560 | c.1191T>C | synonymous_variant | 0.81 |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.9 |
rpoC | 764575 | c.1206T>G | synonymous_variant | 0.92 |
rpoC | 764576 | p.Ser403Ala | missense_variant | 0.92 |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.93 |
rpoC | 764585 | p.Leu406Ile | missense_variant | 0.93 |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.94 |
rpoC | 764611 | c.1242G>C | synonymous_variant | 0.93 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.91 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.91 |
rpoC | 764672 | p.Gln435Tyr | missense_variant | 0.85 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.84 |
rpoC | 764678 | p.Lys437Arg | missense_variant | 0.84 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.81 |
rpoC | 764701 | c.1332C>G | synonymous_variant | 0.82 |
rpoC | 764705 | p.Leu446Lys | missense_variant | 0.81 |
rpoC | 764716 | c.1347G>T | synonymous_variant | 0.8 |
rpoC | 764737 | c.1368G>C | synonymous_variant | 0.26 |
rpoC | 764844 | p.Ala492Gly | missense_variant | 0.28 |
rpoC | 764851 | c.1482C>T | synonymous_variant | 0.57 |
rpoC | 764858 | p.Leu497Met | missense_variant | 0.68 |
rpoC | 764869 | c.1500C>T | synonymous_variant | 0.68 |
rpoC | 764872 | c.1503A>G | synonymous_variant | 0.68 |
rpoC | 764875 | c.1506C>G | synonymous_variant | 0.67 |
rpoC | 764887 | c.1518G>C | synonymous_variant | 0.65 |
rpoC | 764888 | c.1519T>C | synonymous_variant | 0.64 |
rpoC | 764893 | c.1524T>C | synonymous_variant | 0.65 |
rpoC | 764902 | c.1533C>G | synonymous_variant | 0.66 |
rpoC | 764911 | c.1542A>G | synonymous_variant | 0.7 |
rpoC | 764912 | p.Met515Val | missense_variant | 0.7 |
rpoC | 764918 | p.Val517Ile | missense_variant | 0.7 |
rpoC | 764923 | c.1554A>G | synonymous_variant | 0.7 |
rpoC | 764935 | c.1566T>C | synonymous_variant | 0.67 |
rpoC | 764941 | c.1572G>A | synonymous_variant | 0.7 |
rpoC | 764948 | c.1579T>C | synonymous_variant | 0.73 |
rpoC | 764953 | c.1584G>C | synonymous_variant | 0.75 |
rpoC | 764956 | c.1587T>C | synonymous_variant | 0.76 |
rpoC | 764957 | p.Glu530Thr | missense_variant | 0.76 |
rpoC | 764968 | c.1599T>C | synonymous_variant | 0.75 |
rpoC | 764998 | c.1629G>C | synonymous_variant | 0.48 |
rpoC | 765002 | p.Leu545Val | missense_variant | 0.32 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777352 | p.Arg377Trp | missense_variant | 0.2 |
mmpL5 | 777362 | p.Met373Ile | missense_variant | 0.15 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781832 | c.273T>G | synonymous_variant | 0.13 |
fbiC | 1304076 | c.1146C>T | synonymous_variant | 0.5 |
embR | 1417109 | p.Arg80His | missense_variant | 0.14 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.69 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.79 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.85 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.84 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.82 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.82 |
rrs | 1472243 | n.398G>A | non_coding_transcript_exon_variant | 0.82 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.76 |
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.76 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472277 | n.432C>G | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472279 | n.434T>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.49 |
rrs | 1472349 | n.504A>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472374 | n.529T>A | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.49 |
rrs | 1472390 | n.545T>C | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472414 | n.569C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472599 | n.754G>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.49 |
rrs | 1472648 | n.803G>C | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472673 | n.828T>G | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472697 | n.852T>A | non_coding_transcript_exon_variant | 0.51 |
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.85 |
rrs | 1472714 | n.869A>T | non_coding_transcript_exon_variant | 0.89 |
rrs | 1472716 | n.871C>G | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472827 | n.982G>C | non_coding_transcript_exon_variant | 0.76 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.72 |
rrs | 1472837 | n.992C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472880 | n.1035G>A | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.98 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.98 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.98 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.99 |
rrs | 1472982 | n.1137G>A | non_coding_transcript_exon_variant | 0.99 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.99 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.99 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.99 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.99 |
rrs | 1472996 | n.1151T>C | non_coding_transcript_exon_variant | 0.99 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.99 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.99 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.99 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.99 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.98 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.98 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.97 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.97 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.95 |
rrs | 1473070 | n.1225G>A | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1473084 | n.1239T>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1473131 | n.1286G>A | non_coding_transcript_exon_variant | 0.38 |
rrs | 1473139 | n.1294T>C | non_coding_transcript_exon_variant | 0.83 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.87 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.87 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.9 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.92 |
rrs | 1473201 | n.1356A>T | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473248 | n.1403G>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473249 | n.1404T>C | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.8 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.81 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.84 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.95 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.94 |
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 | 0.94 |
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>T | non_coding_transcript_exon_variant | 0.97 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.97 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.97 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.93 |
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 | 0.93 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.69 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2170226 | c.386delA | frameshift_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
pepQ | 2859897 | c.522C>A | synonymous_variant | 0.12 |
thyX | 3067317 | p.Arg210Leu | missense_variant | 0.13 |
thyX | 3067655 | c.291G>A | synonymous_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612029 | p.Ala363Val | missense_variant | 0.13 |
clpC1 | 4038773 | c.1932T>C | synonymous_variant | 0.22 |
clpC1 | 4038776 | p.Glu643Asp | missense_variant | 0.24 |
clpC1 | 4038781 | p.Leu642Phe | missense_variant | 0.26 |
clpC1 | 4038795 | p.Ser637Ile | missense_variant | 0.26 |
clpC1 | 4038805 | p.Ile634Val | missense_variant | 0.27 |
clpC1 | 4038806 | p.Glu633Asp | missense_variant | 0.27 |
clpC1 | 4038809 | p.Gln632Pro | missense_variant | 0.27 |
clpC1 | 4038812 | c.1893T>C | synonymous_variant | 0.27 |
clpC1 | 4038835 | p.Phe624Leu | missense_variant | 0.35 |
clpC1 | 4038841 | p.Val622Leu | missense_variant | 0.33 |
clpC1 | 4038845 | c.1858_1860delTCGinsAGC | synonymous_variant | 0.35 |
clpC1 | 4038849 | p.Phe619Tyr | missense_variant | 0.35 |
clpC1 | 4038851 | c.1854G>C | synonymous_variant | 0.36 |
clpC1 | 4038860 | c.1845G>T | synonymous_variant | 0.34 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.33 |
clpC1 | 4038890 | p.Glu605Asp | missense_variant | 0.18 |
clpC1 | 4039674 | p.Pro344Lys | missense_variant | 0.16 |
clpC1 | 4039697 | c.1008C>T | synonymous_variant | 0.62 |
clpC1 | 4039730 | c.975C>G | synonymous_variant | 0.52 |
clpC1 | 4039739 | c.966C>G | synonymous_variant | 0.34 |
clpC1 | 4039742 | c.963C>T | synonymous_variant | 0.22 |
clpC1 | 4040021 | c.684A>G | synonymous_variant | 0.2 |
clpC1 | 4040032 | p.Val225Ile | missense_variant | 0.37 |
clpC1 | 4040033 | c.672G>C | synonymous_variant | 0.27 |
clpC1 | 4040045 | c.660C>G | synonymous_variant | 0.19 |
clpC1 | 4040054 | c.651G>A | synonymous_variant | 0.38 |
embC | 4241562 | p.Arg567His | missense_variant | 0.15 |
embC | 4241578 | c.1716G>T | synonymous_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4245645 | p.Ala805Ser | missense_variant | 0.2 |
embB | 4245854 | c.-660C>A | upstream_gene_variant | 0.15 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |