Vitis vinifera vs Glycine max LastZ Results

Back to all analyses

Vitis vinifera (Vitis vinifera, IGGP_12x) and Glycine max (Glycine max, V1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 210,929

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 403,733,628 out of 486,265,422
Covered: 82,531,794 out of 486,265,422

Uncovered: 4,338,695 out of 32,794,161
Matches: 20,118,731 out of 32,794,161
Mismatches: 7,730,511 out of 32,794,161
Insertions: 606,224 out of 32,794,161

Glycine max

Uncovered: 924,031,980 out of 973,344,380
Covered: 49,312,400 out of 973,344,380

Uncovered: 39,820,122 out of 64,476,920
Matches: 17,562,696 out of 64,476,920
Mismatches: 6,601,325 out of 64,476,920
Insertions: 492,777 out of 64,476,920

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)