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Oryza sativa Japonica Group vs Ananas comosus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Ananas comosus (Ananas comosus, F153) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 GroupAnanas comosus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 152,037 alignment blocks

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

Uncovered: 332,610,423 out of 375,049,285
Covered: 42,438,862 out of 375,049,285

Uncovered: 9,142,640 out of 34,424,450
Matches: 17,407,512 out of 34,424,450
Mismatches: 7,150,390 out of 34,424,450
Insertions: 723,908 out of 34,424,450
Identity over aligned base-pairs: 68.9%

Ananas comosus

Uncovered: 279,872,965 out of 315,839,004
Covered: 35,966,039 out of 315,839,004

Uncovered: 5,850,447 out of 27,915,811
Matches: 15,308,581 out of 27,915,811
Mismatches: 6,181,719 out of 27,915,811
Insertions: 575,064 out of 27,915,811
Identity over aligned base-pairs: 69.4%

Block size distribution

Size range All 152,037 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,534
7.9 kb
10 bp - 100 bp
22,200
1.5 Mb
5,070
356.9 kb
100 bp - 1 kb
119,073
39.6 Mb
29,788
11.2 Mb
1 kb - 10 kb
9,230
14.1 Mb
15,571
36.6 Mb
10 kb - 100 kb
307
5.4 Mb
100 kb - 1 Mb
9
1.5 Mb