Prunus persica vs Arabidopsis thaliana LastZ Results

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Prunus persica (Prunus persica, Prupe1_0) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Prunus persica 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: 147,640

Genome coverage (bp) Coding exon coverage (bp)
Prunus persica

Uncovered: 186,765,143 out of 227,251,827
Covered: 40,486,684 out of 227,251,827

Uncovered: 8,833,608 out of 33,830,599
Matches: 16,766,554 out of 33,830,599
Mismatches: 7,522,635 out of 33,830,599
Insertions: 707,802 out of 33,830,599

Arabidopsis thaliana

Uncovered: 81,930,283 out of 119,667,750
Covered: 37,737,467 out of 119,667,750

Uncovered: 6,876,064 out of 33,462,323
Matches: 18,164,768 out of 33,462,323
Mismatches: 7,872,574 out of 33,462,323
Insertions: 548,917 out of 33,462,323

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

Prunus persica Arabidopsis thaliana
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}