VEP run statistics

--check_svs --custom /scratch.global/pmorrell/Context_of_Mutations/Gmax_275_Wm82.a2.v1.gene_exons_sorted.gff3.gz,,gff --fasta /panfs/roc/groups/9/morrellp/shared/References/Reference_Sequences/Soybean/PhytozomeV11/Gmax/assembly/Gmax_275_v2.0.fa --force_overwrite --format vcf --gff /scratch.global/pmorrell/Context_of_Mutations/Gmax_275_Wm82.a2.v1.gene_exons_sorted.gff3.gz --input_file /panfs/roc/groups/9/morrellp/shared/Projects/Context_Of_Mutations/analysis/de_novo/filtered/BL107_final_filtered_nomis_rare.vcf --output_file BL107_VeP_rare.txt --species glycine_max --total_length --verbose --warning_file BL107_vep_err_rare.txt

General statistics

Variant classes

Consequences (most severe)

Consequences (all)

Coding consequences

Variants by chromosome

Distribution of variants on chromosome Chr01

Distribution of variants on chromosome Chr02

Distribution of variants on chromosome Chr03

Distribution of variants on chromosome Chr04

Distribution of variants on chromosome Chr05

Distribution of variants on chromosome Chr06

Distribution of variants on chromosome Chr07

Distribution of variants on chromosome Chr08

Distribution of variants on chromosome Chr09

Distribution of variants on chromosome Chr10

Distribution of variants on chromosome Chr11

Distribution of variants on chromosome Chr12

Distribution of variants on chromosome Chr13

Distribution of variants on chromosome Chr14

Distribution of variants on chromosome Chr15

Distribution of variants on chromosome Chr16

Distribution of variants on chromosome Chr17

Distribution of variants on chromosome Chr18

Distribution of variants on chromosome Chr19

Distribution of variants on chromosome Chr20

Distribution of variants on chromosome scaffold_1038

Distribution of variants on chromosome scaffold_105

Distribution of variants on chromosome scaffold_1057

Distribution of variants on chromosome scaffold_1065

Distribution of variants on chromosome scaffold_1078

Distribution of variants on chromosome scaffold_110

Distribution of variants on chromosome scaffold_111

Distribution of variants on chromosome scaffold_1118

Distribution of variants on chromosome scaffold_1160

Distribution of variants on chromosome scaffold_1179

Distribution of variants on chromosome scaffold_119

Distribution of variants on chromosome scaffold_123

Distribution of variants on chromosome scaffold_1233

Distribution of variants on chromosome scaffold_1241

Distribution of variants on chromosome scaffold_1271

Distribution of variants on chromosome scaffold_128

Distribution of variants on chromosome scaffold_1317

Distribution of variants on chromosome scaffold_1321

Distribution of variants on chromosome scaffold_1327

Distribution of variants on chromosome scaffold_137

Distribution of variants on chromosome scaffold_138

Distribution of variants on chromosome scaffold_139

Distribution of variants on chromosome scaffold_1394

Distribution of variants on chromosome scaffold_151

Distribution of variants on chromosome scaffold_152

Distribution of variants on chromosome scaffold_157

Distribution of variants on chromosome scaffold_164

Distribution of variants on chromosome scaffold_168

Distribution of variants on chromosome scaffold_1718

Distribution of variants on chromosome scaffold_1742

Distribution of variants on chromosome scaffold_1745

Distribution of variants on chromosome scaffold_186

Distribution of variants on chromosome scaffold_191

Distribution of variants on chromosome scaffold_1967

Distribution of variants on chromosome scaffold_197

Distribution of variants on chromosome scaffold_205

Distribution of variants on chromosome scaffold_208

Distribution of variants on chromosome scaffold_21

Distribution of variants on chromosome scaffold_211

Distribution of variants on chromosome scaffold_2140

Distribution of variants on chromosome scaffold_216

Distribution of variants on chromosome scaffold_22

Distribution of variants on chromosome scaffold_223

Distribution of variants on chromosome scaffold_229

Distribution of variants on chromosome scaffold_23

Distribution of variants on chromosome scaffold_24

Distribution of variants on chromosome scaffold_25

Distribution of variants on chromosome scaffold_263

Distribution of variants on chromosome scaffold_265

Distribution of variants on chromosome scaffold_27

Distribution of variants on chromosome scaffold_28

Distribution of variants on chromosome scaffold_296

Distribution of variants on chromosome scaffold_30

Distribution of variants on chromosome scaffold_31

Distribution of variants on chromosome scaffold_32

Distribution of variants on chromosome scaffold_344

Distribution of variants on chromosome scaffold_345

Distribution of variants on chromosome scaffold_353

Distribution of variants on chromosome scaffold_36

Distribution of variants on chromosome scaffold_361

Distribution of variants on chromosome scaffold_376

Distribution of variants on chromosome scaffold_40

Distribution of variants on chromosome scaffold_409

Distribution of variants on chromosome scaffold_41

Distribution of variants on chromosome scaffold_426

Distribution of variants on chromosome scaffold_44

Distribution of variants on chromosome scaffold_442

Distribution of variants on chromosome scaffold_471

Distribution of variants on chromosome scaffold_484

Distribution of variants on chromosome scaffold_521

Distribution of variants on chromosome scaffold_530

Distribution of variants on chromosome scaffold_587

Distribution of variants on chromosome scaffold_608

Distribution of variants on chromosome scaffold_614

Distribution of variants on chromosome scaffold_623

Distribution of variants on chromosome scaffold_636

Distribution of variants on chromosome scaffold_681

Distribution of variants on chromosome scaffold_691

Distribution of variants on chromosome scaffold_711

Distribution of variants on chromosome scaffold_713

Distribution of variants on chromosome scaffold_72

Distribution of variants on chromosome scaffold_73

Distribution of variants on chromosome scaffold_74

Distribution of variants on chromosome scaffold_744

Distribution of variants on chromosome scaffold_75

Distribution of variants on chromosome scaffold_76

Distribution of variants on chromosome scaffold_78

Distribution of variants on chromosome scaffold_843

Distribution of variants on chromosome scaffold_846

Distribution of variants on chromosome scaffold_88

Distribution of variants on chromosome scaffold_896

Distribution of variants on chromosome scaffold_91

Distribution of variants on chromosome scaffold_93

Distribution of variants on chromosome scaffold_97

Distribution of variants on chromosome scaffold_99

Position in protein