We must define the word "complete". To me, "complete" means comparing the "compete" human genome with the "complete" chimp genome. This was not done.
Is was done for 94% of the Chimpanzee genome with constituted 98% of all the DNA information that was of high quality...i.e. devoid of precisely those kinds of contaminants you were complaining about in the other post. From the paper:-
"
The draft genome assembly—generated from ~3.6-fold sequence redundancy of the autosomes and ~1.8-fold redundancy of both sex chromosomes—covers ~94% of the chimpanzee genome with >98% of the sequence in high-quality bases. A total of 50% of the sequence (N50) is contained in contigs of length greater than 15.7 kilobases (kb) and supercontigs of length greater than 8.6 megabases (Mb). The assembly represents a consensus of two haplotypes, with one allele from each heterozygous position arbitrarily represented in the sequence."
And hence they say
"Thus, by restricting our analysis to (these) high-quality bases, the nucleotide-level accuracy of the WGS assembly is essentially equal to that of ‘finished’ sequence."
You do not want to analyze those parts (about 6%) that do are not as accurately determined do you? Are you pinning your hopes that this 6% of the genome will reveal revolutionary differences?
Nature (2005): Initial sequence of the chimpanzee genome and comparison with the human genome
"Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a LARGELY COMPLETE CATALOGUE OF GENETIC DIFFERENCES that have accumulated since the human and chimpanzee species diverged from our common ancestor..."
Note: A COMPLETE catalogue of ALL differences? This is a lie. The comparison was done AFTER they removed significant differences between the two genomes - differences so significant that they could not be aligned side-by-side in the first place or where there was too much 'overlap'.
"Thus, by restricting our analysis to high-quality bases, the nucleotide-level accuracy of the WGS assembly is essentially equal to that of ‘finished’ sequence."
The quote-mining is noted. The high quality bases cover 94% of all genome that they themselves say just a paragraph ago! Are you doing the quote mining, or are you copy-pasting from another lying creationist blurb?
"“Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ~2.4 gigabases (Gb) of high-quality sequence”
Ah! More quote mining!
Here is the entire paragraph
"
Nucleotide divergence
Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ~2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y.
Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies
12, 33, 34. The differences between one copy of the human genome and one copy of the chimpanzee genome include both the sites of fixed divergence between the species and some polymorphic sites within each species. "
Thus while 2.4 Gb (out of a total 2.9 Gb) align exactly, the overall divergence in alignment is 1.23%. This supports your case, how exactly? Strange you do not quote the very next sentence! Who is bending the truth now!
"The combined alignments were chained and only best reciprocal alignments were retained for further analysis."
Yet another isolated quote. Two seperate programs were used to make the alignment between human and chimp genes and only those sequences where the predictions of both programs were matched were retained. That is
why they are only talking about 94% of the chimp genome. The other 6% were rejected through various quality filters!
"
BLASTZ154 was used to align non-repetitive chimpanzee regions against repeat-masked human sequence. BLAT155 was subsequently used to align the more repetitive regions. The combined alignments were chained156 and only best reciprocal alignments were retained for further analysis."
Note: they admit only using 'best-fit' sections of DNA for their analysis - aka cherry-picking the data to get the 'best' result, thus artificially increasing similarity between the two DNA sections. This, in turn, artificially increases overall similarity between chimps and humans.
Absolutely false. See what they actually say above. You would know this if you read the line just before the paper.
Have you read it, and if you have read it, why are you lying?
Finally let me quote from the supplementary section to show that the quotes above refer only to alignment methods and not to select how much was being studied
"Genome Alignment. We evaluated three independent methods for aligning chimpanzee contigs to human genome sequence. The first utilized BLASTZ (Schwartz 2003) to align and score non-repetitive chimpanzee regions against repeat-masked human sequence and BLAT (Kent 2002) to process the more repetitive regions. Alignment chains differentiated between orthologous and paralogous alignments (Kent 2003) and only “reciprocal best” alignments were retained in the alignment set.
In the second method, each contig was aligned to human sequence with a hashing procedure based on affine Smith-Waterman calculations for locally refining alignments without repeat masking (D. Jaffe and T.S. Mikkelsen, unpublished). Each alignment was assigned a confidence value based on alignment strength and frequency.
The last method split chimp contigs into 1 kb segments and aligned them to human sequence with BLAT. This step was followed by re-alignment using cross_match (P. Green, personal communication) to exploit base quality values and tagging of unique alignments. "
The supplementary section goes on to say that they chose the first method as it was found to be most reliable. The section also says after an exhaustive survey of this and many other details of the methods theys used
"
We estimate the genome coverage to be about 94%, based on comparison to 12 finished CHORI-251 BAC clones. These clones collectively comprise a total of 1,265,617 bases of sequence. Table S11 shows detailed information of these comparisons.
Specifically, ARACHNE covers 1,186,774 bases, or 93.8% of the clones, while PCAP covers 1,189,836 bases, or 94.0% of the clones. "
Here is a brief explanation the article gives on how the chimp and human DNA sequences were 'screened' PRIOR to comparison (ref: Found under 'Supplemental Notes' of article):
"All alignments in the >90% and >60% categories were examined if the chimp scaffold spanned more than 1.5 times its counterpart in the human genome. When the offending supercontig only subsumed other supercontigs less than 1.5 kb, they were retained. For those that would completely overlap large contigs, the alignments were manually reviewed to determine if the alignment should be broken.
At this point scaffolds spanning a total of 2.85 Gb were anchored to the human genome sequence (excluding those in the random bins). All scaffolds that were completely overlapped by another scaffold based on the human position were then removed. Also removed were the smaller of two neighboring contigs when there was an overlap of 60% (based on human) between neighboring scaffolds. The total anchored sequence after these steps dropped to 2.74 Gb (2.41 Gb of actual contig length), or 88% of the total chimpanzee sequence."
No. This is a misunderstanding. This entire method was used to determine those sections that were
exactly aligned. As has been said in the main paper
"
"
Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ~2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y.
Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies
12, 33, 34. The differences between one copy of the human genome and one copy of the chimpanzee genome include both the sites of fixed divergence between the species and some polymorphic sites within each species. "
In short, while 88% of the genome was exactly align-able to the human genome, the degree of variation within the genome was based on the entire 94% of the genome that was considered to be good quality and was used for study. That variation is about 1% for single nucleotide changes and 4% if group insertion, deletions and replications are considered.
You have misunderstood the results completely. For what reason i do not know. The first paragraph of the paper says this explicitly
"Because the chimpanzee lies at such a short evolutionary distance with respect to human,
nearly all of the bases are identical by descent and sequences can be readily aligned except in recently derived, large repetitive regions. The focus thus turns to differences rather than similarities."
Sections where these repetitions are present cannot be aligned in a global scale. These repetitions are 4% of the differences globally and cause this misalignment. See? Very clear.