Run ID: SRR13861149
Sample name:
Date: 03-04-2023 09:24:42
Number of reads: 201978
Percentage reads mapped: 3.37
Strain: lineage4.9
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 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761131 | p.Gly442Glu | missense_variant | 0.75 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5532 | c.295dupG | frameshift_variant | 1.0 |
gyrB | 5832 | p.Ala198Gly | missense_variant | 1.0 |
gyrA | 6976 | c.-326A>G | upstream_gene_variant | 1.0 |
ccsA | 619735 | c.-156G>C | upstream_gene_variant | 1.0 |
ccsA | 620100 | c.210G>T | synonymous_variant | 1.0 |
rpoB | 759609 | c.-198C>A | upstream_gene_variant | 1.0 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.5 |
rpoB | 761126 | c.1320G>T | synonymous_variant | 0.75 |
rpoB | 761129 | c.1323G>C | synonymous_variant | 0.75 |
rpoB | 761133 | p.Leu443Ile | missense_variant | 0.75 |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.82 |
rpoB | 761151 | p.Leu449Val | missense_variant | 0.82 |
rpoB | 761156 | c.1350G>C | synonymous_variant | 0.82 |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.82 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.82 |
rpoB | 761168 | c.1362C>G | synonymous_variant | 0.82 |
rpoB | 761178 | p.Ser458Thr | missense_variant | 0.82 |
rpoB | 761192 | c.1386C>G | synonymous_variant | 0.82 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.82 |
rpoB | 761196 | p.Leu464Phe | missense_variant | 0.82 |
rpoB | 761204 | c.1398C>T | synonymous_variant | 0.75 |
rpoB | 761207 | c.1401C>T | synonymous_variant | 0.75 |
rpoB | 761213 | c.1407G>A | synonymous_variant | 0.75 |
rpoB | 761220 | p.Ser472Thr | missense_variant | 0.75 |
rpoB | 761234 | c.1428G>C | synonymous_variant | 0.75 |
rpoB | 761235 | p.Met477Val | missense_variant | 0.75 |
rpoC | 762860 | c.-510G>C | upstream_gene_variant | 0.4 |
rpoC | 762863 | c.-507T>C | upstream_gene_variant | 0.4 |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.5 |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.5 |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.5 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.5 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.6 |
rpoC | 762929 | c.-441G>C | upstream_gene_variant | 0.5 |
rpoB | 762930 | p.Pro1042Ser | missense_variant | 0.5 |
rpoC | 762936 | c.-434_-432delTCGinsAGC | upstream_gene_variant | 0.5 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.43 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.43 |
rpoC | 762962 | c.-408C>T | upstream_gene_variant | 0.6 |
rpoC | 762971 | c.-399G>A | upstream_gene_variant | 0.5 |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.5 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.5 |
rpoC | 762995 | c.-375G>T | upstream_gene_variant | 0.5 |
rpoC | 763050 | c.-320C>T | upstream_gene_variant | 1.0 |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.4 |
rpoC | 764401 | c.1032C>T | synonymous_variant | 0.5 |
rpoC | 764404 | c.1035C>T | synonymous_variant | 0.5 |
rpoC | 764405 | c.1036A>C | synonymous_variant | 0.5 |
rpoC | 764419 | c.1050C>T | synonymous_variant | 0.44 |
rpoC | 764428 | c.1059G>T | synonymous_variant | 0.44 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.57 |
rpoC | 764435 | c.1066_1068delAGGinsCGC | synonymous_variant | 0.57 |
rpoC | 764441 | p.Ile358Leu | missense_variant | 0.57 |
rpoC | 764446 | c.1077T>C | synonymous_variant | 0.5 |
rpoC | 764451 | p.Gly361Ala | missense_variant | 0.5 |
rpoC | 764455 | c.1086G>T | synonymous_variant | 0.5 |
rpoC | 764461 | p.Glu364Asp | missense_variant | 0.5 |
rpoC | 764470 | c.1101C>G | synonymous_variant | 0.5 |
rpoC | 764471 | p.Asn368Arg | missense_variant | 0.5 |
rpoC | 764479 | c.1110G>A | synonymous_variant | 0.5 |
rpoC | 764485 | c.1116G>C | synonymous_variant | 0.5 |
rpoC | 764498 | p.Ser377Ala | missense_variant | 0.5 |
rpoC | 764503 | c.1134G>C | synonymous_variant | 0.5 |
rpoC | 764509 | c.1140G>C | synonymous_variant | 0.5 |
rpoC | 764513 | p.Phe382Leu | missense_variant | 0.5 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.5 |
rpoC | 764527 | c.1158C>T | synonymous_variant | 0.33 |
mmpL5 | 776796 | p.Val562Ala | missense_variant | 1.0 |
mmpS5 | 779584 | c.-679A>C | upstream_gene_variant | 0.29 |
Rv1258c | 1407009 | p.Ala111Asp | missense_variant | 1.0 |
rrs | 1472094 | n.249T>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472108 | n.263C>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472128 | n.283G>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472133 | n.288G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.74 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.74 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.81 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.81 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.81 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.84 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.76 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.76 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.94 |
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 | 0.93 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.54 |
inhA | 1674891 | p.Trp230Cys | missense_variant | 1.0 |
tlyA | 1918625 | p.Pro229Leu | missense_variant | 1.0 |
Rv1979c | 2222721 | c.444G>C | synonymous_variant | 1.0 |
ahpC | 2726345 | p.Phe51Leu | missense_variant | 1.0 |
Rv2752c | 3067095 | c.-904G>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448912 | p.Ile137Phe | missense_variant | 1.0 |
fprA | 3474133 | p.Pro43Thr | missense_variant | 1.0 |
whiB7 | 3568676 | p.Ser2Ala | missense_variant | 1.0 |
alr | 3840783 | c.637_638insT | frameshift_variant | 1.0 |
clpC1 | 4038326 | p.Glu793Asp | missense_variant | 1.0 |
embC | 4241026 | c.1164C>G | synonymous_variant | 1.0 |
embA | 4242250 | c.-983C>G | upstream_gene_variant | 1.0 |
embB | 4247398 | c.885G>T | synonymous_variant | 1.0 |
aftB | 4267490 | c.1347G>C | synonymous_variant | 1.0 |
ethA | 4326203 | p.Ser424* | stop_gained | 1.0 |