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Oryza sativa Japonica Group vs Ipomoea triloba LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

Chunking parameters

ParameterOryza sativa Japonica GroupIpomoea triloba
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 159,398 alignment blocks

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

Uncovered: 340,566,479 out of 375,049,285
Covered: 34,482,806 out of 375,049,285

Uncovered: 13,905,469 out of 34,818,902
Matches: 13,542,495 out of 34,818,902
Mismatches: 6,815,690 out of 34,818,902
Insertions: 555,248 out of 34,818,902
Identity over aligned base-pairs: 64.8%

Ipomoea triloba

Uncovered: 423,876,450 out of 461,827,428
Covered: 37,950,978 out of 461,827,428

Uncovered: 14,687,552 out of 39,533,495
Matches: 16,260,432 out of 39,533,495
Mismatches: 8,015,852 out of 39,533,495
Insertions: 569,659 out of 39,533,495
Identity over aligned base-pairs: 65.4%

Block size distribution

Size range All 159,398 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,248
6.0 kb
10 bp - 100 bp
25,717
1.8 Mb
5,908
423.2 kb
100 bp - 1 kb
123,967
40.0 Mb
35,953
14.2 Mb
1 kb - 10 kb
8,439
12.6 Mb
18,702
38.9 Mb
10 kb - 100 kb
27
672.7 kb
81
1.6 Mb