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Emiliania huxleyi vs Bigelowiella natans LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Emiliania huxleyi 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

ParameterEmiliania huxleyiBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 12,503 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi

Uncovered: 165,514,896 out of 167,675,649
Covered: 2,160,753 out of 167,675,649

Uncovered: 38,023,499 out of 39,740,234
Matches: 1,089,047 out of 39,740,234
Mismatches: 577,097 out of 39,740,234
Insertions: 50,591 out of 39,740,234
Identity over aligned base-pairs: 63.4%

Bigelowiella natans

Uncovered: 93,375,148 out of 94,701,163
Covered: 1,326,015 out of 94,701,163

Uncovered: 27,637,301 out of 28,817,508
Matches: 727,729 out of 28,817,508
Mismatches: 420,605 out of 28,817,508
Insertions: 31,873 out of 28,817,508
Identity over aligned base-pairs: 61.7%

Block size distribution

Size range All 12,503 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
49
254.0 bp
10 bp - 100 bp
4,733
326.8 kb
1,066
76.8 kb
100 bp - 1 kb
7,477
1.9 Mb
4,047
1.4 Mb
1 kb - 10 kb
243
396.9 kb
603
1.1 Mb
10 kb - 100 kb
1
10.1 kb
2
24.3 kb