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Oryza sativa Japonica Group vs Secale cereale LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Secale cereale (Secale cereale, Rye_Lo7_2018_v1p1p1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. 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 GroupSecale cereale
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 352,099 alignment blocks

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

Uncovered: 294,784,593 out of 375,049,285
Covered: 80,264,692 out of 375,049,285

Uncovered: 3,642,772 out of 34,424,450
Matches: 23,825,019 out of 34,424,450
Mismatches: 6,112,400 out of 34,424,450
Insertions: 844,259 out of 34,424,450
Identity over aligned base-pairs: 77.4%

Secale cereale

Uncovered: 6,585,643,520 out of 6,735,227,109
Covered: 149,583,589 out of 6,735,227,109

Uncovered: 4,148,604 out of 44,182,623
Matches: 30,960,041 out of 44,182,623
Mismatches: 8,178,948 out of 44,182,623
Insertions: 895,030 out of 44,182,623
Identity over aligned base-pairs: 77.3%

Block size distribution

Size range All 352,099 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,492
13.9 kb
10 bp - 100 bp
50,089
3.3 Mb
23,917
1.7 Mb
100 bp - 1 kb
250,562
93.0 Mb
124,201
44.6 Mb
1 kb - 10 kb
48,931
83.2 Mb
48,641
118.6 Mb
10 kb - 100 kb
24
527.8 kb
1,056
15.0 Mb
100 kb - 1 Mb
1
100.7 kb
2
283.1 kb