Vitis vinifera vs Physcomitrella patens LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Physcomitrella patens (Physcomitrella patens, Phypa_V3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 viniferaPhyscomitrella patens
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 122,081 alignment blocks

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

Uncovered: 465,402,238 out of 486,265,422
Covered: 20,863,184 out of 486,265,422

Uncovered: 19,139,628 out of 32,794,161
Matches: 8,696,779 out of 32,794,161
Mismatches: 4,712,561 out of 32,794,161
Insertions: 245,193 out of 32,794,161
Identity over aligned base-pairs: 63.7%

Physcomitrella patens

Uncovered: 452,970,698 out of 471,852,792
Covered: 18,882,094 out of 471,852,792

Uncovered: 21,053,048 out of 34,318,961
Matches: 8,570,803 out of 34,318,961
Mismatches: 4,424,362 out of 34,318,961
Insertions: 270,748 out of 34,318,961
Identity over aligned base-pairs: 64.6%

Block size distribution

Size range All 122,081 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
929
4.5 kb
10 bp - 100 bp
24,634
1.8 Mb
5,813
426.6 kb
100 bp - 1 kb
93,776
25.9 Mb
33,557
12.7 Mb
1 kb - 10 kb
2,742
3.9 Mb
10,025
18.3 Mb
10 kb - 100 kb
11
134.6 kb