Oryza sativa Japonica vs Physcomitrella patens LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Physcomitrella patens (Physcomitrella patens, ASM242v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica 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: 70,017

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

Uncovered: 357,736,807 out of 374,424,240
Covered: 16,687,433 out of 374,424,240

Uncovered: 22,768,373 out of 34,124,807
Matches: 7,272,722 out of 34,124,807
Mismatches: 3,860,982 out of 34,124,807
Insertions: 222,730 out of 34,124,807

Physcomitrella patens

Uncovered: 469,385,011 out of 479,985,347
Covered: 10,600,336 out of 479,985,347

Uncovered: 27,180,725 out of 34,827,652
Matches: 4,900,750 out of 34,827,652
Mismatches: 2,569,906 out of 34,827,652
Insertions: 176,271 out of 34,827,652

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)