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Oryza sativa Japonica Group vs Camelina sativa LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Camelina sativa (Camelina sativa, Cs) 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 GroupCamelina sativa
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 324,421 alignment blocks

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

Uncovered: 333,644,070 out of 375,049,285
Covered: 41,405,215 out of 375,049,285

Uncovered: 14,422,756 out of 34,424,450
Matches: 12,115,361 out of 34,424,450
Mismatches: 7,357,692 out of 34,424,450
Insertions: 528,641 out of 34,424,450
Identity over aligned base-pairs: 60.6%

Camelina sativa

Uncovered: 548,212,446 out of 641,356,059
Covered: 93,143,613 out of 641,356,059

Uncovered: 46,751,522 out of 107,028,261
Matches: 39,252,998 out of 107,028,261
Mismatches: 19,830,471 out of 107,028,261
Insertions: 1,193,270 out of 107,028,261
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 324,421 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,811
14.3 kb
10 bp - 100 bp
51,083
3.5 Mb
10,759
780.5 kb
100 bp - 1 kb
250,962
82.1 Mb
76,851
30.1 Mb
1 kb - 10 kb
19,565
32.7 Mb
39,959
85.3 Mb
10 kb - 100 kb
187
2.3 Mb