Arabidopsis thaliana vs Prunus_dulcis LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus_dulcis (Prunus dulcis, ALMONDv2) 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: 127,490

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

Uncovered: 83,164,320 out of 119,667,750
Covered: 36,503,430 out of 119,667,750

Uncovered: 7,989,733 out of 33,775,569
Matches: 17,572,928 out of 33,775,569
Mismatches: 7,681,499 out of 33,775,569
Insertions: 531,409 out of 33,775,569

Prunus dulcis

Uncovered: 188,425,367 out of 227,498,357
Covered: 39,072,990 out of 227,498,357

Uncovered: 9,826,657 out of 33,980,404
Matches: 16,248,809 out of 33,980,404
Mismatches: 7,201,956 out of 33,980,404
Insertions: 702,982 out of 33,980,404

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