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Oryza sativa Japonica Group vs Prunus persica LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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
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

Chunking parameters

ParameterOryza sativa Japonica GroupPrunus persica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 135,742 alignment blocks

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

Uncovered: 341,457,938 out of 375,049,285
Covered: 33,591,347 out of 375,049,285

Uncovered: 13,680,784 out of 34,403,043
Matches: 13,504,208 out of 34,403,043
Mismatches: 6,726,159 out of 34,403,043
Insertions: 491,892 out of 34,403,043
Identity over aligned base-pairs: 65.2%

Prunus persica

Uncovered: 196,387,515 out of 227,411,381
Covered: 31,023,866 out of 227,411,381

Uncovered: 12,239,021 out of 33,236,255
Matches: 13,677,817 out of 33,236,255
Mismatches: 6,834,782 out of 33,236,255
Insertions: 484,635 out of 33,236,255
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 135,742 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,004
4.9 kb
10 bp - 100 bp
21,124
1.5 Mb
4,593
328.8 kb
100 bp - 1 kb
105,846
34.3 Mb
28,694
11.4 Mb
1 kb - 10 kb
7,767
11.5 Mb
16,179
34.8 Mb
10 kb - 100 kb
1
10.0 kb
59
757.1 kb