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Oryza sativa Japonica Group vs Prunus dulcis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Prunus dulcis (Prunus dulcis, ALMONDv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 GroupPrunus dulcis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options

Statistics over 134,518 alignment blocks

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

Uncovered: 341,648,411 out of 375,049,285
Covered: 33,400,874 out of 375,049,285

Uncovered: 14,043,268 out of 34,818,902
Matches: 13,534,953 out of 34,818,902
Mismatches: 6,753,387 out of 34,818,902
Insertions: 487,294 out of 34,818,902
Identity over aligned base-pairs: 65.1%

Prunus dulcis

Uncovered: 196,516,095 out of 227,498,357
Covered: 30,982,262 out of 227,498,357

Uncovered: 13,593,267 out of 33,980,404
Matches: 13,318,905 out of 33,980,404
Mismatches: 6,599,498 out of 33,980,404
Insertions: 468,734 out of 33,980,404
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 134,518 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,015
5.0 kb
10 bp - 100 bp
20,858
1.4 Mb
4,262
305.7 kb
100 bp - 1 kb
104,838
34.1 Mb
27,870
11.1 Mb
1 kb - 10 kb
7,800
11.7 Mb
16,280
35.0 Mb
10 kb - 100 kb
7
102.5 kb
66
871.1 kb