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Phaeodactylum tricornutum vs Bigelowiella natans LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,309 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 26,549,274 out of 27,568,093
Covered: 1,018,819 out of 27,568,093

Uncovered: 16,912,252 out of 17,873,974
Matches: 590,420 out of 17,873,974
Mismatches: 341,109 out of 17,873,974
Insertions: 30,193 out of 17,873,974
Identity over aligned base-pairs: 61.4%

Bigelowiella natans

Uncovered: 93,611,359 out of 94,701,163
Covered: 1,089,804 out of 94,701,163

Uncovered: 27,821,391 out of 28,817,508
Matches: 617,643 out of 28,817,508
Mismatches: 350,484 out of 28,817,508
Insertions: 27,990 out of 28,817,508
Identity over aligned base-pairs: 62.0%

Block size distribution

Size range All 5,309 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
92.0 bp
10 bp - 100 bp
1,804
125.9 kb
350
25.0 kb
100 bp - 1 kb
3,280
913.8 kb
1,667
660.8 kb
1 kb - 10 kb
210
313.7 kb
389
667.6 kb