Arabidopsis thaliana vs Actinidia chinensis LastZ Results

Back to all analyses

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Actinidia chinensis (Actinidia chinensis var. chinensis, Red5_PS1_1.69.0) 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: 105,806

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

Uncovered: 85,327,221 out of 119,667,750
Covered: 34,340,529 out of 119,667,750

Uncovered: 8,681,592 out of 33,775,569
Matches: 16,982,403 out of 33,775,569
Mismatches: 7,575,974 out of 33,775,569
Insertions: 535,600 out of 33,775,569

Actinidia chinensis var. chinensis

Uncovered: 526,138,457 out of 553,842,477
Covered: 27,704,020 out of 553,842,477

Uncovered: 24,240,912 out of 42,227,027
Matches: 12,229,284 out of 42,227,027
Mismatches: 5,285,145 out of 42,227,027
Insertions: 471,686 out of 42,227,027

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 Actinidia chinensis
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}