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Oryza sativa Japonica Group vs Cucumis sativus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cucumis sativus (Cucumis sativus, ASM407v2) 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
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 GroupCucumis sativus
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 115,125 alignment blocks

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

Uncovered: 345,233,330 out of 375,049,285
Covered: 29,815,955 out of 375,049,285

Uncovered: 15,783,771 out of 34,818,902
Matches: 12,325,236 out of 34,818,902
Mismatches: 6,297,336 out of 34,818,902
Insertions: 412,559 out of 34,818,902
Identity over aligned base-pairs: 64.7%

Cucumis sativus

Uncovered: 169,672,768 out of 193,829,320
Covered: 24,156,552 out of 193,829,320

Uncovered: 9,552,551 out of 26,192,424
Matches: 10,843,109 out of 26,192,424
Mismatches: 5,462,557 out of 26,192,424
Insertions: 334,207 out of 26,192,424
Identity over aligned base-pairs: 65.2%

Block size distribution

Size range All 115,125 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
824
3.9 kb
10 bp - 100 bp
18,110
1.3 Mb
3,619
258.9 kb
100 bp - 1 kb
90,595
28.7 Mb
23,885
9.7 Mb
1 kb - 10 kb
5,596
8.2 Mb
13,415
27.9 Mb
10 kb - 100 kb
30
373.7 kb