Vitis vinifera vs Rosa chinensis LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. Vitis vinifera 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

ParameterVitis viniferaRosa chinensis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 286,190 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 424,167,664 out of 486,265,422
Covered: 62,097,758 out of 486,265,422

Uncovered: 4,074,053 out of 32,794,161
Matches: 20,601,918 out of 32,794,161
Mismatches: 7,537,332 out of 32,794,161
Insertions: 580,858 out of 32,794,161
Identity over aligned base-pairs: 71.7%

Rosa chinensis

Uncovered: 435,713,713 out of 515,588,973
Covered: 79,875,260 out of 515,588,973

Uncovered: 8,810,551 out of 43,773,732
Matches: 24,709,599 out of 43,773,732
Mismatches: 9,471,934 out of 43,773,732
Insertions: 781,648 out of 43,773,732
Identity over aligned base-pairs: 70.7%

Block size distribution

Size range All 286,190 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,046
10.8 kb
10 bp - 100 bp
51,353
3.4 Mb
21,456
1.5 Mb
100 bp - 1 kb
210,588
69.1 Mb
94,562
31.7 Mb
1 kb - 10 kb
22,131
36.4 Mb
23,380
52.7 Mb
10 kb - 100 kb
72
1.2 Mb
529
12.3 Mb
100 kb - 1 Mb
49
12.0 Mb