Oryza sativa Japonica Group vs Panicum hallii HAL2 LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Panicum hallii HAL2 (Panicum hallii var. hallii str. HAL2, PhalliiHAL_v2.1) 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.


Number of alignment blocks: 138,224

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

Uncovered: 294,738,822 out of 375,049,285
Covered: 80,310,463 out of 375,049,285

Uncovered: 3,383,748 out of 34,349,962
Matches: 24,341,294 out of 34,349,962
Mismatches: 5,864,068 out of 34,349,962
Insertions: 760,852 out of 34,349,962

Panicum hallii var. hallii str. HAL2

Uncovered: 421,618,277 out of 487,473,734
Covered: 65,855,457 out of 487,473,734

Uncovered: 8,501,547 out of 37,739,336
Matches: 23,411,899 out of 37,739,336
Mismatches: 5,201,568 out of 37,739,336
Insertions: 624,322 out of 37,739,336

Configuration parameters

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)
     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 Panicum hallii HAL2
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}