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Oryza longistaminata vs Oryza punctata LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza longistaminata 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)3000
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 longistaminataOryza punctata
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 351,746 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 137,100,443 out of 326,442,508
Covered: 189,342,065 out of 326,442,508

Uncovered: 1,571,229 out of 34,512,301
Matches: 30,290,521 out of 34,512,301
Mismatches: 2,293,995 out of 34,512,301
Insertions: 356,556 out of 34,512,301
Identity over aligned base-pairs: 92.0%

Oryza punctata

Uncovered: 237,829,153 out of 393,816,603
Covered: 155,987,450 out of 393,816,603

Uncovered: 7,692,704 out of 39,315,246
Matches: 29,333,774 out of 39,315,246
Mismatches: 1,887,942 out of 39,315,246
Insertions: 400,826 out of 39,315,246
Identity over aligned base-pairs: 92.8%

Block size distribution

Size range All 351,746 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,407
33.8 kb
10 bp - 100 bp
67,662
4.1 Mb
27,047
1.8 Mb
100 bp - 1 kb
229,355
83.2 Mb
78,402
28.0 Mb
1 kb - 10 kb
49,173
109.0 Mb
14,274
32.8 Mb
10 kb - 100 kb
149
1.7 Mb
2,504
85.7 Mb
100 kb - 1 Mb
297
49.9 Mb