Run ID: ERR2229707
Sample name:
Date: 31-03-2023 17:27:57
Number of reads: 599364
Percentage reads mapped: 99.31
Strain: lineage4.8
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8831 | c.1530G>A | synonymous_variant | 0.14 |
fgd1 | 491281 | p.Asp167Asn | missense_variant | 0.25 |
ccsA | 620811 | c.921G>A | synonymous_variant | 0.13 |
rpoB | 759721 | c.-86G>C | upstream_gene_variant | 0.13 |
rpoB | 760690 | p.Phe295Ser | missense_variant | 0.11 |
rpoB | 762433 | p.Gly876Asp | missense_variant | 0.12 |
rpoC | 765181 | c.1812G>A | synonymous_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776080 | p.Ala801Ser | missense_variant | 0.25 |
mmpL5 | 776081 | c.2400G>A | synonymous_variant | 0.17 |
mmpL5 | 776087 | c.2394C>G | synonymous_variant | 0.15 |
mmpL5 | 776093 | c.2386_2388delCGCinsAGA | synonymous_variant | 0.15 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.13 |
mmpL5 | 776103 | p.Ile793Gly | missense_variant | 0.14 |
mmpL5 | 776105 | c.2376G>C | synonymous_variant | 0.14 |
mmpL5 | 777081 | p.Lys467Met | missense_variant | 0.14 |
mmpL5 | 777625 | p.Gln286Lys | missense_variant | 0.12 |
mmpS5 | 779527 | c.-622C>A | upstream_gene_variant | 0.17 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781642 | p.Pro28Gln | missense_variant | 0.14 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
Rv1258c | 1406409 | p.Leu311Pro | missense_variant | 0.29 |
embR | 1417156 | c.191delC | frameshift_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473315 | n.1470T>C | non_coding_transcript_exon_variant | 0.22 |
fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.11 |
fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.12 |
fabG1 | 1673357 | c.-83G>A | upstream_gene_variant | 0.13 |
fabG1 | 1673359 | c.-81T>C | upstream_gene_variant | 0.15 |
fabG1 | 1673361 | c.-79C>G | upstream_gene_variant | 0.15 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.17 |
inhA | 1674346 | p.Arg49Cys | missense_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102293 | c.750C>T | synonymous_variant | 0.14 |
ndh | 2103177 | c.-135G>T | upstream_gene_variant | 0.14 |
katG | 2154369 | c.1743G>A | synonymous_variant | 0.14 |
katG | 2154918 | c.1194G>A | synonymous_variant | 0.14 |
katG | 2156228 | c.-117T>C | upstream_gene_variant | 0.13 |
katG | 2156398 | c.-287C>A | upstream_gene_variant | 0.12 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2169269 | c.1344A>G | synonymous_variant | 0.11 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.12 |
PPE35 | 2169278 | c.1335T>C | synonymous_variant | 0.14 |
PPE35 | 2169281 | c.1332T>G | synonymous_variant | 0.14 |
PPE35 | 2169287 | c.1326T>C | synonymous_variant | 0.12 |
PPE35 | 2169293 | c.1320T>C | synonymous_variant | 0.11 |
PPE35 | 2169308 | c.1305C>T | synonymous_variant | 0.11 |
PPE35 | 2169457 | p.His386Asp | missense_variant | 0.21 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.48 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.48 |
PPE35 | 2170379 | c.234G>T | synonymous_variant | 0.11 |
PPE35 | 2170382 | c.231C>T | synonymous_variant | 0.11 |
PPE35 | 2170469 | c.144G>C | synonymous_variant | 0.1 |
Rv1979c | 2222870 | p.Ala99Thr | missense_variant | 0.33 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518652 | p.His180Asn | missense_variant | 0.17 |
Rv2752c | 3064737 | p.Gln485His | missense_variant | 0.29 |
thyX | 3067431 | p.Arg172Pro | missense_variant | 0.17 |
thyX | 3067607 | p.Asp113Glu | missense_variant | 0.15 |
thyA | 3074173 | p.Ser100Leu | missense_variant | 0.12 |
thyA | 3074544 | c.-73T>G | upstream_gene_variant | 0.22 |
Rv3083 | 3448386 | c.-118C>T | upstream_gene_variant | 0.14 |
fbiB | 3641493 | c.-42T>G | upstream_gene_variant | 0.12 |
fbiB | 3642328 | p.Arg265Gln | missense_variant | 0.12 |
rpoA | 3878087 | p.Glu141Gln | missense_variant | 0.12 |
clpC1 | 4038752 | p.Gln651His | missense_variant | 0.15 |
clpC1 | 4038773 | p.Asp644Glu | missense_variant | 0.17 |
clpC1 | 4038776 | p.Glu643Asp | missense_variant | 0.17 |
clpC1 | 4040271 | p.Tyr145Phe | missense_variant | 0.2 |
embC | 4239878 | c.20delC | frameshift_variant | 0.18 |
embC | 4241063 | p.Ile401Val | missense_variant | 0.18 |
embC | 4241097 | p.Ser412* | stop_gained | 0.15 |
embC | 4241461 | c.1599C>T | synonymous_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242648 | p.Leu929Arg | missense_variant | 0.33 |
embA | 4244519 | c.1287G>C | synonymous_variant | 0.18 |
embA | 4244534 | c.1304delG | frameshift_variant | 0.25 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.19 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.5 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.57 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.57 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.38 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.31 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.25 |
embB | 4247564 | p.Arg351Gly | missense_variant | 0.18 |
embB | 4249035 | p.Arg841Gln | missense_variant | 0.33 |
embB | 4249285 | p.Glu924Asp | missense_variant | 0.14 |
aftB | 4268189 | c.648C>A | synonymous_variant | 0.14 |
aftB | 4268510 | p.Ser109Arg | missense_variant | 0.15 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408281 | c.-79C>T | upstream_gene_variant | 0.13 |
Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 |