Target sequence: Oryzias latipes (Hd-rR (Southern Japanese) strain) Assembly version1.0
Query sequence: Oryzias latipes (HNI (Northern Japanese) strain) Assembly version1.0
We calculated all alignments between the Hd-rR scaffolds and HNI scaffolds using BLAT with "-tileSize=12 -minMatch=3 -repMatch=100 -fastMap" options. We subsequently listed Hd-rR and HNI scaffold pairs that were both more than 2Kbp long and had at least one alignment block of more than or equal to 100bp. The final alignments were produced from these pairs using BLASTZ and related programs used in mouse-human comparison. Repetitive regions detected by RepeatMasker with RepBase Update (version 9.11), were ignored in the seeding phase of BLASTZ but were used in the alignment extension phase.
To eliminate false-positive polymorphism sites, mismatches and gaps were treated
as effective polymorphism candidates if their Phred quality values (QV) were > 30
(for a gap, QV is set to the average value of two adjoining non-gap bases)
and if the QV of the five flanking bases was > 25, and they had no 'N' basecall.
Polymorphisms were selected from the candidates.
The two strains of medaka under analysis had roughly a 3% difference between them at the nucleotide level.
We were able to detect 16.4 million reliable SNPs, 2.85 million insertions and deletions
by aligning the HNI assembly against the Hd-rR assembly.
'.' indicates a "matched" base, colered pink by default.
'A', 'C', 'G' or 'T' show "mismatched" bases between Hd-rR and HNI assemblies, and HNI base is displayed in the image.
'N' means three types of alignment: unsequenced Hd-rR region, Hd-rR region not aligned with HNI sequence and Hd-rR region aligned with HNI sequence but doesn't have enough quality to satisfy filtering criteria. The second case may be caused by deletion in the HNI genome or simply low shotgun sequence coverage of HNI assembly.
This genome browser and track are based on Hd-rR sequence index. So current version of this track can not provide insertion (HNI longer, Hd-rR shorter) information.
Deletion (HNI shorter, Hd-rR longer) is shown by '=' in the image, colored cyan by default.
User can change displaying colers by a track config window.