Oryza sativa Japonica Group vs Corchorus capsularis LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) 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: 123,809

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

Uncovered: 342,838,883 out of 375,049,285
Covered: 32,210,402 out of 375,049,285

Uncovered: 14,783,255 out of 34,403,043
Matches: 12,734,309 out of 34,403,043
Mismatches: 6,441,879 out of 34,403,043
Insertions: 443,600 out of 34,403,043

Corchorus capsularis

Uncovered: 288,516,233 out of 317,178,409
Covered: 28,662,176 out of 317,178,409

Uncovered: 13,040,705 out of 30,371,305
Matches: 11,353,888 out of 30,371,305
Mismatches: 5,607,786 out of 30,371,305
Insertions: 368,926 out of 30,371,305

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 Corchorus capsularis
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}