Arabidopsis thaliana vs Oryza punctata LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 112,119

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,545,811 out of 119,667,750
Covered: 26,121,939 out of 119,667,750

Uncovered: 14,466,129 out of 33,775,569
Matches: 12,534,555 out of 33,775,569
Mismatches: 6,382,154 out of 33,775,569
Insertions: 392,731 out of 33,775,569

Oryza punctata

Uncovered: 364,961,555 out of 393,816,603
Covered: 28,855,048 out of 393,816,603

Uncovered: 19,081,200 out of 39,315,246
Matches: 13,007,337 out of 39,315,246
Mismatches: 6,727,290 out of 39,315,246
Insertions: 499,419 out of 39,315,246

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

Arabidopsis thaliana Oryza punctata
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}