Vitis vinifera vs Setaria italica LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Setaria italica (Setaria italica, Setaria_italica_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: 174,610

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

Uncovered: 446,871,815 out of 486,265,422
Covered: 39,393,607 out of 486,265,422

Uncovered: 10,052,844 out of 32,794,161
Matches: 14,897,122 out of 32,794,161
Mismatches: 7,348,487 out of 32,794,161
Insertions: 495,708 out of 32,794,161

Setaria italica

Uncovered: 369,279,846 out of 405,732,883
Covered: 36,453,037 out of 405,732,883

Uncovered: 15,594,245 out of 39,583,990
Matches: 15,669,643 out of 39,583,990
Mismatches: 7,764,242 out of 39,583,990
Insertions: 555,860 out of 39,583,990

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Setaria italica
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}