Vitis vinifera vs Gossypium raimondii LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Gossypium raimondii (Gossypium raimondii, Graimondii2_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: 264,340

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

Uncovered: 420,661,016 out of 486,265,422
Covered: 65,604,406 out of 486,265,422

Uncovered: 3,656,070 out of 32,794,161
Matches: 20,640,502 out of 32,794,161
Mismatches: 7,903,874 out of 32,794,161
Insertions: 593,715 out of 32,794,161

Gossypium raimondii

Uncovered: 683,412,585 out of 761,405,269
Covered: 77,992,684 out of 761,405,269

Uncovered: 4,722,253 out of 45,523,048
Matches: 29,202,253 out of 45,523,048
Mismatches: 10,839,832 out of 45,523,048
Insertions: 758,710 out of 45,523,048

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 Gossypium raimondii
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}