Oryza sativa Japonica Group vs Manihot esculenta LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) 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: 158,027

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

Uncovered: 340,030,252 out of 375,049,285
Covered: 35,019,033 out of 375,049,285

Uncovered: 13,951,359 out of 34,403,043
Matches: 13,093,147 out of 34,403,043
Mismatches: 6,896,827 out of 34,403,043
Insertions: 461,710 out of 34,403,043

Manihot esculenta

Uncovered: 543,687,258 out of 582,117,524
Covered: 38,430,266 out of 582,117,524

Uncovered: 13,440,730 out of 38,679,430
Matches: 16,493,922 out of 38,679,430
Mismatches: 8,221,779 out of 38,679,430
Insertions: 522,999 out of 38,679,430

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 Manihot esculenta
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}