Vitis vinifera vs Glycine max LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Glycine max (Glycine max, Glycine_max_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 366,153

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

Uncovered: 423,742,087 out of 486,265,422
Covered: 62,523,335 out of 486,265,422

Uncovered: 4,525,958 out of 32,794,161
Matches: 19,721,614 out of 32,794,161
Mismatches: 7,899,440 out of 32,794,161
Insertions: 647,149 out of 32,794,161

Glycine max

Uncovered: 869,696,153 out of 978,416,860
Covered: 108,720,707 out of 978,416,860

Uncovered: 10,435,122 out of 65,631,894
Matches: 39,263,754 out of 65,631,894
Mismatches: 14,894,644 out of 65,631,894
Insertions: 1,038,374 out of 65,631,894

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
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)--ambiguous=iupac

Chunking parameters

Vitis vinifera Glycine max
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}