In this section

Oryza sativa Japonica Group vs Digitaria exilis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Digitaria exilis (Digitaria exilis, Fonio_CM05836) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 107. 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 GroupDigitaria exilis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 351,035 alignment blocks

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

Uncovered: 292,557,649 out of 375,049,285
Covered: 82,491,636 out of 375,049,285

Uncovered: 3,428,303 out of 34,424,450
Matches: 23,986,480 out of 34,424,450
Mismatches: 6,210,286 out of 34,424,450
Insertions: 799,381 out of 34,424,450
Identity over aligned base-pairs: 77.4%

Digitaria exilis

Uncovered: 567,757,732 out of 716,471,022
Covered: 148,713,290 out of 716,471,022

Uncovered: 11,287,778 out of 62,841,479
Matches: 39,995,651 out of 62,841,479
Mismatches: 10,198,929 out of 62,841,479
Insertions: 1,359,121 out of 62,841,479
Identity over aligned base-pairs: 77.6%

Block size distribution

Size range All 351,035 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,794
24.3 kb
10 bp - 100 bp
65,171
3.6 Mb
14,627
1.0 Mb
100 bp - 1 kb
230,857
87.9 Mb
66,159
22.4 Mb
1 kb - 10 kb
50,202
85.9 Mb
22,238
51.0 Mb
10 kb - 100 kb
11
153.9 kb
441
10.3 Mb
100 kb - 1 Mb
29
12.1 Mb
1 Mb - 10 Mb
24
80.7 Mb