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Oryza sativa Japonica Group vs Citrullus lanatus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Citrullus lanatus (Citrullus lanatus, Cla97_v1) 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 GroupCitrullus lanatus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 120,842 alignment blocks

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

Uncovered: 344,148,825 out of 375,049,285
Covered: 30,900,460 out of 375,049,285

Uncovered: 15,300,174 out of 34,424,450
Matches: 12,401,980 out of 34,424,450
Mismatches: 6,292,132 out of 34,424,450
Insertions: 430,164 out of 34,424,450
Identity over aligned base-pairs: 64.8%

Citrullus lanatus

Uncovered: 340,733,550 out of 365,450,462
Covered: 24,716,912 out of 365,450,462

Uncovered: 9,384,807 out of 26,302,942
Matches: 11,068,764 out of 26,302,942
Mismatches: 5,508,635 out of 26,302,942
Insertions: 340,736 out of 26,302,942
Identity over aligned base-pairs: 65.4%

Block size distribution

Size range All 120,842 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,004
4.7 kb
10 bp - 100 bp
19,831
1.4 Mb
4,555
319.7 kb
100 bp - 1 kb
94,432
29.6 Mb
26,099
10.3 Mb
1 kb - 10 kb
5,553
8.2 Mb
13,707
28.1 Mb
10 kb - 100 kb
22
354.2 kb
54
783.8 kb