Run ID: ERR4820394
Sample name:
Date: 01-04-2023 16:39:37
Number of reads: 806496
Percentage reads mapped: 44.8
Strain: lineage4.3.4.2.1
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
tlyA | 1917946 | p.Arg3* | stop_gained | 0.1 | capreomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 575930 | p.Glu195Lys | missense_variant | 0.17 |
rpoB | 760907 | p.Phe367Leu | missense_variant | 0.12 |
rpoB | 762185 | c.2379G>C | synonymous_variant | 0.12 |
rpoB | 762206 | c.2400C>G | synonymous_variant | 0.13 |
rpoB | 762209 | c.2403C>G | synonymous_variant | 0.13 |
rpoB | 762218 | c.2412T>C | synonymous_variant | 0.14 |
rpoB | 762243 | p.Arg813Lys | missense_variant | 0.12 |
rpoB | 762251 | c.2445G>C | synonymous_variant | 0.12 |
rpoB | 762254 | c.2448T>C | synonymous_variant | 0.12 |
rpoB | 762266 | c.2460T>C | synonymous_variant | 0.1 |
rpoC | 762863 | c.-507T>C | upstream_gene_variant | 0.14 |
rpoB | 762872 | p.Met1022Ile | missense_variant | 0.21 |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.23 |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.24 |
rpoC | 762894 | c.-476C>T | upstream_gene_variant | 0.2 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.19 |
rpoB | 762925 | p.Thr1040Ile | missense_variant | 0.18 |
rpoC | 762929 | c.-441G>C | upstream_gene_variant | 0.19 |
rpoC | 762932 | c.-438G>C | upstream_gene_variant | 0.19 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.19 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.19 |
rpoC | 762962 | c.-408C>T | upstream_gene_variant | 0.18 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.17 |
rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.19 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.19 |
rpoC | 762995 | c.-375G>C | upstream_gene_variant | 0.2 |
rpoC | 764070 | p.Leu234Pro | missense_variant | 0.13 |
rpoC | 764377 | c.1008C>G | synonymous_variant | 0.12 |
rpoC | 764380 | c.1011G>C | synonymous_variant | 0.13 |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.2 |
rpoC | 764392 | c.1023C>T | synonymous_variant | 0.19 |
rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.19 |
rpoC | 764410 | c.1041G>C | synonymous_variant | 0.17 |
rpoC | 764428 | c.1059G>C | synonymous_variant | 0.14 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.14 |
rpoC | 764435 | c.1066A>C | synonymous_variant | 0.14 |
rpoC | 764446 | p.Asp359Glu | missense_variant | 0.17 |
rpoC | 764450 | p.Gly361Arg | missense_variant | 0.16 |
rpoC | 764455 | c.1086G>C | synonymous_variant | 0.17 |
rpoC | 764458 | c.1089G>C | synonymous_variant | 0.17 |
rpoC | 764461 | p.Glu364Asp | missense_variant | 0.17 |
rpoC | 764470 | c.1101C>G | synonymous_variant | 0.17 |
rpoC | 764471 | p.Asn368Arg | missense_variant | 0.17 |
rpoC | 764485 | c.1116G>C | synonymous_variant | 0.36 |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.38 |
rpoC | 764498 | p.Ser377Ala | missense_variant | 0.38 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.32 |
rpoC | 764527 | c.1158C>G | synonymous_variant | 0.28 |
rpoC | 764533 | c.1164C>G | synonymous_variant | 0.29 |
rpoC | 764537 | p.Pro390Ala | missense_variant | 0.29 |
rpoC | 764540 | p.Val391Ile | missense_variant | 0.29 |
rpoC | 764543 | c.1176delC | frameshift_variant | 0.29 |
rpoC | 764549 | c.1181_1182delCG | frameshift_variant | 0.29 |
rpoC | 764553 | p.Gly395Ala | missense_variant | 0.29 |
rpoC | 764557 | c.1188_1189insAAG | conservative_inframe_insertion | 0.31 |
rpoC | 764560 | c.1191T>G | synonymous_variant | 0.31 |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.41 |
rpoC | 764575 | c.1206T>C | synonymous_variant | 0.53 |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.53 |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.53 |
rpoC | 764587 | c.1218C>G | synonymous_variant | 0.53 |
rpoC | 764623 | c.1254C>G | synonymous_variant | 0.38 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.29 |
rpoC | 764641 | c.1272C>T | synonymous_variant | 0.29 |
rpoC | 764644 | c.1275G>C | synonymous_variant | 0.27 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.25 |
rpoC | 764656 | c.1287C>G | synonymous_variant | 0.25 |
rpoC | 764665 | c.1296C>G | synonymous_variant | 0.24 |
rpoC | 764668 | c.1299C>T | synonymous_variant | 0.22 |
rpoC | 764671 | c.1302G>C | synonymous_variant | 0.21 |
rpoC | 764672 | p.Gln435Glu | missense_variant | 0.21 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.2 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.17 |
rpoC | 764701 | c.1332C>G | synonymous_variant | 0.17 |
rpoC | 764705 | p.Leu446Lys | missense_variant | 0.17 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
rpoC | 766441 | c.3072C>A | synonymous_variant | 0.2 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776169 | p.Gly771Val | missense_variant | 0.18 |
mmpL5 | 779280 | c.-800G>A | upstream_gene_variant | 0.11 |
mmpS5 | 779596 | c.-693_-692dupAC | upstream_gene_variant | 0.1 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472954 | n.1109T>C | 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 | 1472970 | n.1125C>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472974 | n.1129A>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472975 | n.1130T>G | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472993 | n.1148G>A | non_coding_transcript_exon_variant | 0.6 |
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>G | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1473038 | n.1193A>C | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.67 |
fabG1 | 1674176 | p.Gly246Asp | missense_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
thyA | 3074648 | c.-177T>G | upstream_gene_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
fbiA | 3641083 | p.Pro181Ser | missense_variant | 0.12 |
alr | 3840719 | c.702A>G | synonymous_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.89 |
clpC1 | 4039996 | p.Glu237Lys | missense_variant | 0.12 |
panD | 4043938 | p.Ile115Thr | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
aftB | 4268278 | p.Pro187Thr | missense_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
gid | 4408192 | p.Ile4Asn | missense_variant | 0.12 |