Arabidopsis thaliana vs Pistacia vera LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Pistacia vera (Pistacia vera, PisVer_v2) 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: 195,980

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

Uncovered: 81,437,206 out of 119,667,750
Covered: 38,230,544 out of 119,667,750

Uncovered: 7,313,153 out of 33,775,569
Matches: 18,105,469 out of 33,775,569
Mismatches: 7,749,801 out of 33,775,569
Insertions: 607,146 out of 33,775,569

Pistacia vera

Uncovered: 605,107,907 out of 671,152,441
Covered: 66,044,534 out of 671,152,441

Uncovered: 7,936,046 out of 38,113,229
Matches: 20,478,210 out of 38,113,229
Mismatches: 8,903,582 out of 38,113,229
Insertions: 795,391 out of 38,113,229

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 Pistacia vera
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options