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Oryza sativa Japonica Group vs Cucumis melo LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cucumis melo (Cucumis melo, Melonv4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 GroupCucumis melo
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 125,664 alignment blocks

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

Uncovered: 344,748,898 out of 375,049,285
Covered: 30,300,387 out of 375,049,285

Uncovered: 15,541,419 out of 34,424,450
Matches: 12,240,831 out of 34,424,450
Mismatches: 6,234,026 out of 34,424,450
Insertions: 408,174 out of 34,424,450
Identity over aligned base-pairs: 64.8%

Cucumis melo

Uncovered: 331,434,842 out of 357,857,370
Covered: 26,422,528 out of 357,857,370

Uncovered: 11,224,275 out of 27,459,425
Matches: 10,577,049 out of 27,459,425
Mismatches: 5,325,022 out of 27,459,425
Insertions: 333,079 out of 27,459,425
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 125,664 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
878
4.2 kb
10 bp - 100 bp
20,664
1.4 Mb
4,683
334.8 kb
100 bp - 1 kb
98,206
30.8 Mb
29,113
11.3 Mb
1 kb - 10 kb
5,916
8.6 Mb
14,204
28.8 Mb
10 kb - 100 kb
29
355.5 kb