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Oryza sativa Japonica Group vs Nymphaea colorata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Nymphaea colorata (Nymphaea colorata, ASM883128v1) 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 GroupNymphaea colorata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 141,653 alignment blocks

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

Uncovered: 343,888,592 out of 375,049,285
Covered: 31,160,693 out of 375,049,285

Uncovered: 14,324,784 out of 34,424,450
Matches: 13,183,121 out of 34,424,450
Mismatches: 6,393,148 out of 34,424,450
Insertions: 523,397 out of 34,424,450
Identity over aligned base-pairs: 65.6%

Nymphaea colorata

Uncovered: 377,541,697 out of 408,396,728
Covered: 30,855,031 out of 408,396,728

Uncovered: 14,408,233 out of 32,910,518
Matches: 12,074,594 out of 32,910,518
Mismatches: 5,944,226 out of 32,910,518
Insertions: 483,465 out of 32,910,518
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 141,653 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,111
5.1 kb
10 bp - 100 bp
23,616
1.7 Mb
6,904
493.0 kb
100 bp - 1 kb
109,988
34.1 Mb
37,446
14.1 Mb
1 kb - 10 kb
6,938
10.8 Mb
15,436
30.1 Mb
10 kb - 100 kb
104
1.9 Mb