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Arabidopsis thaliana vs Rosa chinensis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. Arabidopsis thaliana 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

ParameterArabidopsis thalianaRosa chinensis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 176,523 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 83,284,751 out of 119,667,750
Covered: 36,382,999 out of 119,667,750

Uncovered: 8,106,481 out of 33,775,569
Matches: 17,449,044 out of 33,775,569
Mismatches: 7,649,364 out of 33,775,569
Insertions: 570,680 out of 33,775,569
Identity over aligned base-pairs: 68.0%

Rosa chinensis

Uncovered: 463,078,403 out of 515,588,973
Covered: 52,510,570 out of 515,588,973

Uncovered: 14,400,042 out of 43,773,732
Matches: 19,595,053 out of 43,773,732
Mismatches: 8,961,557 out of 43,773,732
Insertions: 817,080 out of 43,773,732
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 176,523 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,459
8.3 kb
10 bp - 100 bp
28,854
1.9 Mb
8,591
619.1 kb
100 bp - 1 kb
132,831
44.8 Mb
47,081
16.9 Mb
1 kb - 10 kb
13,375
20.4 Mb
19,728
45.1 Mb
10 kb - 100 kb
4
58.8 kb
290
4.5 Mb
100 kb - 1 Mb
1
111.0 kb