Vitis vinifera vs Leersia perrieri LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) 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: 150,896

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

Uncovered: 451,426,752 out of 486,265,422
Covered: 34,838,670 out of 486,265,422

Uncovered: 11,100,114 out of 32,794,161
Matches: 14,223,020 out of 32,794,161
Mismatches: 6,992,886 out of 32,794,161
Insertions: 478,141 out of 32,794,161

Leersia perrieri

Uncovered: 235,419,351 out of 266,687,832
Covered: 31,268,481 out of 266,687,832

Uncovered: 14,996,174 out of 36,898,596
Matches: 14,304,964 out of 36,898,596
Mismatches: 7,084,372 out of 36,898,596
Insertions: 513,086 out of 36,898,596

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 Leersia perrieri
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}