Oryza sativa Japonica Group vs Panicum hallii FIL2 LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Panicum hallii FIL2 (Panicum hallii str. FIL2, PHallii_v3.1) 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.

Results

Number of alignment blocks: 138,462

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

Uncovered: 294,498,137 out of 375,049,285
Covered: 80,551,148 out of 375,049,285

Uncovered: 3,357,272 out of 34,349,962
Matches: 24,351,867 out of 34,349,962
Mismatches: 5,878,273 out of 34,349,962
Insertions: 762,550 out of 34,349,962

Panicum hallii str. FIL2

Uncovered: 469,909,587 out of 535,889,049
Covered: 65,979,462 out of 535,889,049

Uncovered: 9,136,467 out of 38,415,885
Matches: 23,426,839 out of 38,415,885
Mismatches: 5,224,298 out of 38,415,885
Insertions: 628,281 out of 38,415,885

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 Panicum hallii FIL2
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}