Run ID: SRR13861222
Sample name:
Date: 03-04-2023 09:26:25
Number of reads: 290999
Percentage reads mapped: 4.85
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 | 0.5 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7346 | p.Ile15Met | missense_variant | 1.0 |
gyrA | 8335 | p.Met345Arg | missense_variant | 1.0 |
gyrA | 9639 | p.Gly780Arg | missense_variant | 1.0 |
fgd1 | 491505 | c.723G>A | synonymous_variant | 1.0 |
mshA | 576310 | p.Ile321Met | missense_variant | 1.0 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.22 |
rpoB | 761126 | c.1320G>T | synonymous_variant | 0.5 |
rpoB | 761129 | c.1323G>C | synonymous_variant | 0.5 |
rpoB | 761133 | p.Leu443Ile | missense_variant | 0.5 |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.5 |
rpoB | 761151 | p.Leu449Val | missense_variant | 0.5 |
rpoB | 761156 | c.1350G>C | synonymous_variant | 0.47 |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.47 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.47 |
rpoB | 761168 | c.1362C>G | synonymous_variant | 0.47 |
rpoB | 761178 | p.Ser458Thr | missense_variant | 0.45 |
rpoB | 761192 | c.1386C>G | synonymous_variant | 0.5 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.5 |
rpoB | 761196 | p.Leu464Phe | missense_variant | 0.5 |
rpoB | 761204 | c.1398C>T | synonymous_variant | 0.56 |
rpoB | 761207 | c.1401C>T | synonymous_variant | 0.53 |
rpoB | 761213 | c.1407G>A | synonymous_variant | 0.56 |
rpoB | 761220 | p.Ser472Thr | missense_variant | 0.56 |
rpoB | 761234 | c.1428G>C | synonymous_variant | 0.56 |
rpoB | 761235 | p.Met477Val | missense_variant | 0.56 |
rpoB | 761258 | c.1452G>A | synonymous_variant | 0.3 |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.36 |
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 | 0.53 |
rpoC | 764428 | c.1059G>T | synonymous_variant | 0.53 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.53 |
rpoC | 764435 | c.1066_1068delAGGinsCGC | synonymous_variant | 0.53 |
rpoC | 764441 | p.Ile358Leu | missense_variant | 0.5 |
rpoC | 764446 | c.1077T>C | synonymous_variant | 0.47 |
rpoC | 764451 | p.Gly361Ala | missense_variant | 0.47 |
rpoC | 764455 | c.1086G>T | synonymous_variant | 0.45 |
rpoC | 764461 | p.Glu364Asp | missense_variant | 0.47 |
rpoC | 764470 | c.1101C>G | synonymous_variant | 0.45 |
rpoC | 764471 | p.Asn368Arg | missense_variant | 0.45 |
rpoC | 764479 | c.1110G>A | synonymous_variant | 0.45 |
rpoC | 764485 | c.1116G>C | synonymous_variant | 0.45 |
rpoC | 764498 | p.Ser377Ala | missense_variant | 0.47 |
rpoC | 764503 | c.1134G>C | synonymous_variant | 0.47 |
rpoC | 764509 | c.1140G>C | synonymous_variant | 0.47 |
rpoC | 764513 | p.Phe382Leu | missense_variant | 0.47 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.47 |
rpoC | 764527 | c.1158C>T | synonymous_variant | 0.29 |
rpoC | 766648 | p.Asp1093Glu | missense_variant | 0.25 |
mmpL5 | 775981 | p.Leu834Val | missense_variant | 1.0 |
mmpL5 | 776732 | c.1749C>T | synonymous_variant | 1.0 |
mmpL5 | 777942 | p.Pro180Leu | missense_variant | 1.0 |
fbiC | 1303422 | c.492A>G | synonymous_variant | 1.0 |
Rv1258c | 1406592 | p.Tyr250Cys | missense_variant | 1.0 |
embR | 1416737 | p.Arg204Gln | missense_variant | 1.0 |
rrs | 1472094 | n.249T>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472108 | n.263C>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472128 | n.283G>C | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472133 | n.288G>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.56 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475277 | n.1620G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.9 |
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 | 0.91 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.46 |
rpsA | 1834091 | p.Val184Met | missense_variant | 1.0 |
tlyA | 1918473 | c.534T>A | synonymous_variant | 1.0 |
Rv1979c | 2221849 | p.Leu439Gln | missense_variant | 1.0 |
Rv1979c | 2222231 | p.Met312Leu | missense_variant | 1.0 |
Rv1979c | 2222710 | p.Asn152Ile | missense_variant | 1.0 |
eis | 2714723 | p.Cys204Gly | missense_variant | 1.0 |
folC | 2746975 | p.Asp208Glu | missense_variant | 1.0 |
pepQ | 2860233 | c.186T>G | synonymous_variant | 1.0 |
thyA | 3073781 | p.Leu231Ile | missense_variant | 1.0 |
Rv3083 | 3448420 | c.-84_-83insT | upstream_gene_variant | 1.0 |
whiB7 | 3568689 | c.-11delT | upstream_gene_variant | 1.0 |
embC | 4240494 | p.Gly211Ala | missense_variant | 1.0 |
embC | 4241732 | p.Ala624Pro | missense_variant | 1.0 |
embA | 4245672 | p.Gly814Arg | missense_variant | 1.0 |
embB | 4247458 | p.Tyr315* | stop_gained | 1.0 |
aftB | 4268265 | p.Leu191Gln | missense_variant | 1.0 |