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Oryza sativa Japonica Group vs Malus domestica Golden LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Malus domestica Golden (Malus domestica, ASM211411v1) 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 GroupMalus domestica Golden
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 210,027 alignment blocks

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

Uncovered: 338,970,391 out of 375,049,285
Covered: 36,078,894 out of 375,049,285

Uncovered: 13,175,238 out of 34,424,450
Matches: 13,747,440 out of 34,424,450
Mismatches: 6,943,482 out of 34,424,450
Insertions: 558,290 out of 34,424,450
Identity over aligned base-pairs: 64.7%

Malus domestica Golden

Uncovered: 651,446,021 out of 702,961,352
Covered: 51,515,331 out of 702,961,352

Uncovered: 16,589,007 out of 47,560,911
Matches: 20,347,716 out of 47,560,911
Mismatches: 9,913,239 out of 47,560,911
Insertions: 710,949 out of 47,560,911
Identity over aligned base-pairs: 65.7%

Block size distribution

Size range All 210,027 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,776
8.8 kb
10 bp - 100 bp
36,553
2.5 Mb
9,178
668.0 kb
100 bp - 1 kb
161,004
50.5 Mb
50,002
18.6 Mb
1 kb - 10 kb
10,670
15.9 Mb
23,041
48.9 Mb
10 kb - 100 kb
24
613.1 kb
82
1.3 Mb
100 kb - 1 Mb
1
162.2 kb