Oryza sativa Japonica Group vs Cynara cardunculus LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 156,711

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 344,183,615 out of 375,049,285
Covered: 30,865,670 out of 375,049,285

Uncovered: 15,151,797 out of 34,424,450
Matches: 12,354,976 out of 34,424,450
Mismatches: 6,454,543 out of 34,424,450
Insertions: 463,134 out of 34,424,450

Cynara cardunculus var. scolymus

Uncovered: 692,197,297 out of 724,667,265
Covered: 32,469,968 out of 724,667,265

Uncovered: 11,587,822 out of 32,068,562
Matches: 13,330,839 out of 32,068,562
Mismatches: 6,738,258 out of 32,068,562
Insertions: 411,643 out of 32,068,562

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

Oryza sativa Japonica Group Cynara cardunculus
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}