segments of dna with near - identical sequence ( segmental duplications or duplicons ) in the human genome can be hot spots or predisposition sites for the occurrence of non - allelic homologous recombination or unequal crossing - over leading to genomic mutations such as deletion , duplication , inversion   or translocation . these structural alterations , in turn , can cause dosage imbalance of genetic material or lead to the generation of new gene products resulting in diseases defined as genomic disorders . previous studies to identify segmental duplications in the human genome have analyzed older versions of the genome assembly , which contained higher amounts of unfinished sequence and incorrectly mapped regions , and have used different computational approaches all performed by the same group [ 6 - 8 ] . with the human genome sequence now nearing completion , we have examined its content for segmental duplications using two distinct computational methods . in the first , we utilized the rapid blast2   algorithms that allow direct chromosomal - wide sequence comparisons to be made . all blast results reported in table formats can be subsequently grouped , parsed and analyzed for the detection of duplicated sequences . in addition , we have shown previously that there is a strong correlation between ambiguously mapped snps ( ambsnps ) , as well as the density of snps , and segmental duplications . ambsnps are snps that were annotated to map to two locations on a particular chromosome in the ncbi dbsnp . a subset of these ambsnps are not true snps but are likely to be computer - generated nucleotide mismatches from paralogous copies of duplicated sequences and should be more appropriately labeled as paralogous sequence variants ( psvs ) . another subset is likely to be false ambsnps of genomic sequences that have been misassigned in genome assemblies . here , we report our analysis of all potential psvs in the human genome and their correlation with segmental duplications as detected by our blast analysis . furthermore , we provide a critical assessment on the three latest human genome assemblies from our analysis of sequence misassignments as identified from this study . on the basis of the june 2002 ( ncbi build 30 ) human genome assembly , a total of 107.4 mb ( 3.53% ) of the human genome content ( 3,043.1 mb ) were found to be involved in recent segmental duplications by our blast analysis criteria ( table 1 ) . this content is composed of more than 1,530 distinct intrachromosomal segmental duplications ( 80.3 mb or 2.64% of the total genome , figure 1 ) and 1,637 distinct interchromosomal duplications ( 43.8 mb or 1.44% of the total genome ) . in addition , 29% of all duplications are located in unfinished regions of the current genome assembly . we have also found that 38% of the duplications ( 52.3 mb ) can be considered as tandem duplications - defined here as two related duplicons separated by less than 200 kb . in this study , we only analyzed large ( size  5 kb ) and recent ( sequence identity  90% ) duplications because we can achieve higher confidence and to prioritize those regions for their potential involvement in diseases . previously , bailey and colleagues   reported a total of 5.2% of the human genome involved in recent segmental duplications . the 1.6% discrepancy between our findings could be due to the difference in our detection criteria ( size cutoff of 5 kb used in this study versus 1 kb used in bailey et al . ) . moreover , we have identified 38.9 mb of sequences ( 1.28% of the june 2002 genome assembly ) likely to be artifactual duplications resulting from sequence misassignment errors present in the assembly . by comparing our results with those published previously , we found that 482/2579 clones that we identified to be involved in duplication were novel . the molecular mechanism by which segmental duplications are created is still unclear at the moment . a recent report has suggested that alu repeat clusters had a role as mediators of recurrent chromosomal rearrangements . we have examined whether elevated amounts of repetitive elements could be found in duplicon junctions . we inspected all duplication borders from our results and calculated the occurrence of different repeat types within the 500 bp window outside each duplicon junction . the whole - genome average frequencies were determined by sampling random 500 bp windows across the genome ( excluding gap regions ) . overall , we found that there are significant enrichment ( or relative fold increase ) for the presence of small ribonucleoprotein rna ( srprna ) , satellite , long terminal ( ltr ) and sine / alu repeats ( see additional data file ) . in addition , our data also showed that for some chromosomes the amount of duplicated sequence is higher in the pericentromeric and subtelomeric regions of chromosomes ( figure 1 ) , supporting the hypothesis that these repeat - dense regions have made an important contribution to the evolution of the human genome . regions containing recently occurring segmental duplications can harbor rapidly evolving hominoid - specific genes , as well as novel gene families that are unique to primates . using the national center for biotechnology information refseq annotation of these , 475 genes were fully contained within duplicated regions and were best candidates for recent whole - gene duplication . we have carried out functional analysis of these 475 genes using the gene ontology consortium database   and found that there is a significant increase in gene duplications for genes involved in immune defense ( antibodies , blood - group antigens ) and reproduction ( pregnancy , sex differentiation ) ( see additional data file ) . we were aware that in silico detection methods , such as the ones used in this study , would not allow us to distinguish completely true duplications from artifactual duplications arising from misassigned sequences , especially in cases where sequence identity between two detected duplications exceeded 99.5% over a substantial length ( > 5 kb ) in regions composed of draft sequences . although a small proportion of such results ( duplications with > 99.5% identity ) might represent unfinished regions of the genome that contain true duplications that have arisen very recently in the evolution of the human genome ( such as the large and nearly perfect palindromic repeats located in the azfc region on chromosome yq11.223 involved in male infertility ) , we suspect that most of the duplications ( > 99.5% identity and contain draft sequences ) are in fact sequence misassignment errors in the genome assembly . an explanation for such errors would be when two identical sequences belonging to the same genomic location were misassigned to distinct regions in the genome assembly . we have used the ncbi e - pcr   to evaluate our results ( potential sequence misassignment errors ) from the june 2002 human genome assembly . using some of the largest interchromosomal misassignment errors detected in our study , we found that none of the sts markers located within these misassigned sequences maps to their incorrectly assigned chromosomes . for example , ac121339 is incorrectly mapped to 3q13.13 in the june 2002 genome assembly , as supported by a consensus number of chromosome x sequence - tagged site ( sts ) markers ( figure 2 , table 2 ) . from this genome assembly , we identified that a total of 38.9 mb of sequences , representing 1.28% of the total sequence content , are involved in such potential errors ( a full list of potentially misassigned sequences can be obtained from ) that would require additional effort and further sequencing to achieve resolutions . we also analyzed an additional two previous versions of the human genome assemblies , december 2001 and april 2002 , and our results showed that there has been a dramatic reduction in potential errors in the latest human genome assembly compared to the two previous genome assemblies ( table 3 ) . furthermore , we examined the distribution of the amount of duplications in five different categories on the basis of their level of sequence identity to each other ( table 3 ) . we observed a large reduction in duplications that fall within the 98 - 100% category , supporting the fact that the genome assemblies continue to improve and correct errors made . in addition , our data showed that there have been major improvements for chromosomes 5 , 6 , 7 , 13 , 14 and 19 over the last three genome assemblies . and for chromosomes that had reached finished status , such as chromosomes 20 , 21 and 22 ambsnps are snps that were annotated to map to two locations on a particular chromosome in the ncbi dbsnp . here we show on a genome scale that ambsnps most specifically correlate with intrachromosomal segmental duplications , suggesting they are paralogous sequence variants ( psvs ) ( figure 1 ) . these psvs were perhaps mistakenly introduced into dbsnp by automated in silico - generated analysis , arising from nucleotide mismatches in paralogous copies of duplicated sequences . overall , a surprisingly high proportion , 8.6% ( 199,965 of 2,327,473 ) , of the refsnps were annotated as ambsnps from dbsnp ( build 108 ) . a significant number of the ambsnps ( 139,974 of 199,965 or 70.0% ) are located within duplicated regions as identified by blast and should be regarded as psvs ( see additional data file ) . the non - identification by blast analysis of regions that contain ambsnps first , the duplicated copy(s ) could have been removed from the sequence assembly or the two have been conflated , that is , mistakenly thought to be the same sequence owing to their high sequence similarity . a second possibility is that the duplication is smaller than 5 kb and was excluded in our blast analysis . a third possibility is that a collection of ambsnps could have been generated from misassigned sequences ( identical sequences but misassigned to two difference locations in the genome ) in older assembly builds due to sequencing errors or true snps ( with high polymorphism rate ) in the sequence . we also observed that the density of ambsnps generally correlates with the size of the putative duplication , although this might be affected by the level of sequence identity between duplications . for example , two duplicated sequences sharing 98% sequence identity compared to 95% over the same length might contain fewer psvs as the number of base - pair mismatches would be fewer in the former . in addition , we observed that regions identified by our blast method but that do not contain ambsnps often correspond to artifactual duplications generated from assembly errors . the size , orientation , and contents of segmental duplications are highly variable and most of them show great organizational complexity . this is perhaps due to successive transposition and rearrangement events leading to the creation of segmental duplications . in many cases , for example , one of the largest segmental duplicons detected in this study was 359 kb in size at the williams - beuren locus on 7q11.23 . in this case , the two duplicons are separated by 1.6 mb of intervening sequence with the telomeric duplicon comprising several separate smaller modules as compared to the primary duplicon . the results presented in our study ( provided in tables available at ) would also allow rapid identification of new duplicons that are potentially responsible for chromosome rearrangements and genomic disorders . for example , the location of the duplicons on chromosomes 9q34/22 q11 that have been suggested to mediate recombination leading to the philadelphia chromosome   was identified in our analysis , as were other medically relevant chromosomal regions ( table 4 ) . the characterization of most large segmental duplications is complicated by the fact that many of them ( 29% of all duplications ) are only represented as draft sequences from the current genome assembly . despite the fact that both blast and psvs analyses allowed us to identify most segmental duplications involved in known genomic disorder mutations ( table 4 ) , estimations of the size of rearranged regions were different from those previously reported . in fact , with the exception of several small duplications and the segmental duplications on chromosome 22 , other regions containing duplications involved in genomic disorders were often erroneously assembled and misplaced . furthermore , we have searched the celera human genome c3 ( publicly released version ) and c4 ( subscription - based version ) sequence assemblies for large duplications found on chromosome 7 . we observed that most of them were not represented in large scaffolds , but instead were located in their sequence gaps , or only partially found at ends of scaffolds leading into gaps ( see table 4 ) . this suggests that the whole - genome assembly approach   alone might not be able to finish such duplicated regions in mammalian genomes . on the basis of the june 2002 ( ncbi build 30 ) human genome assembly , a total of 107.4 mb ( 3.53% ) of the human genome content ( 3,043.1 mb ) were found to be involved in recent segmental duplications by our blast analysis criteria ( table 1 ) . this content is composed of more than 1,530 distinct intrachromosomal segmental duplications ( 80.3 mb or 2.64% of the total genome , figure 1 ) and 1,637 distinct interchromosomal duplications ( 43.8 mb or 1.44% of the total genome ) . in addition , 29% of all duplications are located in unfinished regions of the current genome assembly . we have also found that 38% of the duplications ( 52.3 mb ) can be considered as tandem duplications - defined here as two related duplicons separated by less than 200 kb . in this study , we only analyzed large ( size  5 kb ) and recent ( sequence identity  90% ) duplications because we can achieve higher confidence and to prioritize those regions for their potential involvement in diseases . previously , bailey and colleagues   reported a total of 5.2% of the human genome involved in recent segmental duplications . the 1.6% discrepancy between our findings could be due to the difference in our detection criteria ( size cutoff of 5 kb used in this study versus 1 kb used in bailey et al . ) . moreover , we have identified 38.9 mb of sequences ( 1.28% of the june 2002 genome assembly ) likely to be artifactual duplications resulting from sequence misassignment errors present in the assembly . by comparing our results with those published previously , we found that 482/2579 clones that we identified to be involved in duplication were novel . the molecular mechanism by which segmental duplications are created is still unclear at the moment . a recent report has suggested that alu repeat clusters had a role as mediators of recurrent chromosomal rearrangements . we have examined whether elevated amounts of repetitive elements could be found in duplicon junctions . we inspected all duplication borders from our results and calculated the occurrence of different repeat types within the 500 bp window outside each duplicon junction . the whole - genome average frequencies were determined by sampling random 500 bp windows across the genome ( excluding gap regions ) . overall , we found that there are significant enrichment ( or relative fold increase ) for the presence of small ribonucleoprotein rna ( srprna ) , satellite , long terminal ( ltr ) and sine / alu repeats ( see additional data file ) . in addition , our data also showed that for some chromosomes the amount of duplicated sequence is higher in the pericentromeric and subtelomeric regions of chromosomes ( figure 1 ) , supporting the hypothesis that these repeat - dense regions have made an important contribution to the evolution of the human genome . regions containing recently occurring segmental duplications can harbor rapidly evolving hominoid - specific genes , as well as novel gene families that are unique to primates . using the national center for biotechnology information refseq annotation of these , 475 genes were fully contained within duplicated regions and were best candidates for recent whole - gene duplication . we have carried out functional analysis of these 475 genes using the gene ontology consortium database   and found that there is a significant increase in gene duplications for genes involved in immune defense ( antibodies , blood - group antigens ) and reproduction ( pregnancy , sex differentiation ) ( see additional data file ) . we were aware that in silico detection methods , such as the ones used in this study , would not allow us to distinguish completely true duplications from artifactual duplications arising from misassigned sequences , especially in cases where sequence identity between two detected duplications exceeded 99.5% over a substantial length ( > 5 kb ) in regions composed of draft sequences . although a small proportion of such results ( duplications with > 99.5% identity ) might represent unfinished regions of the genome that contain true duplications that have arisen very recently in the evolution of the human genome ( such as the large and nearly perfect palindromic repeats located in the azfc region on chromosome yq11.223 involved in male infertility ) , we suspect that most of the duplications ( > 99.5% identity and contain draft sequences ) are in fact sequence misassignment errors in the genome assembly . an explanation for such errors would be when two identical sequences belonging to the same genomic location were misassigned to distinct regions in the genome assembly . we have used the ncbi e - pcr   to evaluate our results ( potential sequence misassignment errors ) from the june 2002 human genome assembly . using some of the largest interchromosomal misassignment errors detected in our study , we found that none of the sts markers located within these misassigned sequences maps to their incorrectly assigned chromosomes . for example , ac121339 is incorrectly mapped to 3q13.13 in the june 2002 genome assembly , as supported by a consensus number of chromosome x sequence - tagged site ( sts ) markers ( figure 2 , table 2 ) . from this genome assembly , we identified that a total of 38.9 mb of sequences , representing 1.28% of the total sequence content , are involved in such potential errors ( a full list of potentially misassigned sequences can be obtained from ) that would require additional effort and further sequencing to achieve resolutions . we also analyzed an additional two previous versions of the human genome assemblies , december 2001 and april 2002 , and our results showed that there has been a dramatic reduction in potential errors in the latest human genome assembly compared to the two previous genome assemblies ( table 3 ) . furthermore , we examined the distribution of the amount of duplications in five different categories on the basis of their level of sequence identity to each other ( table 3 ) . we observed a large reduction in duplications that fall within the 98 - 100% category , supporting the fact that the genome assemblies continue to improve and correct errors made . in addition , our data showed that there have been major improvements for chromosomes 5 , 6 , 7 , 13 , 14 and 19 over the last three genome assemblies . and for chromosomes that had reached finished status , such as chromosomes 20 , 21 and 22 , the number of errors was negligible . ambsnps are snps that were annotated to map to two locations on a particular chromosome in the ncbi dbsnp . here we show on a genome scale that ambsnps most specifically correlate with intrachromosomal segmental duplications , suggesting they are paralogous sequence variants ( psvs ) ( figure 1 ) . these psvs were perhaps mistakenly introduced into dbsnp by automated in silico - generated analysis , arising from nucleotide mismatches in paralogous copies of duplicated sequences . overall , a surprisingly high proportion , 8.6% ( 199,965 of 2,327,473 ) , of the refsnps were annotated as ambsnps from dbsnp ( build 108 ) . a significant number of the ambsnps ( 139,974 of 199,965 or 70.0% ) are located within duplicated regions as identified by blast and should be regarded as psvs ( see additional data file ) . the non - identification by blast analysis of regions that contain ambsnps could be due to one of three possibilities . first , the duplicated copy(s ) could have been removed from the sequence assembly or the two have been conflated , that is , mistakenly thought to be the same sequence owing to their high sequence similarity . a second possibility is that the duplication is smaller than 5 kb and was excluded in our blast analysis . a third possibility is that a collection of ambsnps could have been generated from misassigned sequences ( identical sequences but misassigned to two difference locations in the genome ) in older assembly builds due to sequencing errors or true snps ( with high polymorphism rate ) in the sequence . we also observed that the density of ambsnps generally correlates with the size of the putative duplication , although this might be affected by the level of sequence identity between duplications . for example , two duplicated sequences sharing 98% sequence identity compared to 95% over the same length might contain fewer psvs as the number of base - pair mismatches would be fewer in the former . in addition , we observed that regions identified by our blast method but that do not contain ambsnps often correspond to artifactual duplications generated from assembly errors . the size , orientation , and contents of segmental duplications are highly variable and most of them show great organizational complexity . this is perhaps due to successive transposition and rearrangement events leading to the creation of segmental duplications . in many cases , for example , one of the largest segmental duplicons detected in this study was 359 kb in size at the williams - beuren locus on 7q11.23 . in this case , the two duplicons are separated by 1.6 mb of intervening sequence with the telomeric duplicon comprising several separate smaller modules as compared to the primary duplicon . the results presented in our study ( provided in tables available at ) would also allow rapid identification of new duplicons that are potentially responsible for chromosome rearrangements and genomic disorders . for example , the location of the duplicons on chromosomes 9q34/22 q11 that have been suggested to mediate recombination leading to the philadelphia chromosome   was identified in our analysis , as were other medically relevant chromosomal regions ( table 4 ) . the characterization of most large segmental duplications is complicated by the fact that many of them ( 29% of all duplications ) are only represented as draft sequences from the current genome assembly . despite the fact that both blast and psvs analyses allowed us to identify most segmental duplications involved in known genomic disorder mutations ( table 4 ) , estimations of the size of rearranged regions were different from those previously reported . in fact , with the exception of several small duplications and the segmental duplications on chromosome 22 , other regions containing duplications involved in genomic disorders were often erroneously assembled and misplaced . furthermore , we have searched the celera human genome c3 ( publicly released version ) and c4 ( subscription - based version ) sequence assemblies for large duplications found on chromosome 7 . we observed that most of them were not represented in large scaffolds , but instead were located in their sequence gaps , or only partially found at ends of scaffolds leading into gaps ( see table 4 ) . this suggests that the whole - genome assembly approach   alone might not be able to finish such duplicated regions in mammalian genomes . we have used two different computational approaches to identify the locations of all recent segmental duplications in the current human genome draft sequence . the fidelity of the results reflects the quality of the assembly examined and the parameters used . in addition , our approach has detected numerous potential sequence misassignment errors in the current genome annotation , allowing rapid error detection in future sequence assemblies . the segmental duplication map of the human genome should serve as a guide for investigation of the role of duplications in genomic disorders , as well as their contributions to normal human genomic variability . it is clear that genomic regions containing segmental duplications present a major challenge to the completion of the human genome sequence by april 2003 . focused efforts including targeted sequencing of allele - specific clones , high - resolution fluorescence in situ hybridization , and expert curation would be required to validate the actual ( or proposed ) organization of these complex regions as well as to complete the human genome reference sequence . we obtained the december 2001 , april 2002 , and june 2002 ( ncbi build 28 , 29 and 30 respectively ) human genome assemblies through the university of california , santa cruz human genome browser . all chromosome sequences were lower - case masked for highly repetitive elements by repeatmasker ( a.f.a . each of the 25 masked chromosome sequences ( including one unmapped chromosome sequence ' chrun ' ) was compared against itself by chromosome - wide blast2   to detect intrachromosomal segmental duplications ( 25 comparisons made ) , as well as pairwise comparisons to each of the other 24 chromosomes to detect interchromosomal segmental duplications ( 600 comparisons made ) . all blast results were subsequently parsed to eliminate low - quality and fragmented alignments under the following criteria : blast results having  90% sequence identity ,  80 bp in length , and with expected value  10 . all identical hits ( same coordinate alignments ) , including suboptimal blast alignments recognized by multiple , overlapping alignments , as well as mirror hits ( reverse coordinate alignments ) from the blast results of the intrachromosomal set were removed . contiguous alignments separated by a distance of less than 3 kb , then 5 kb , and subsequently 9 kb were joined ( stepwise ) into modules in order to traverse masked repetitive sequences and to overcome breaks in the blast alignments caused by insertions / deletions and sequence gaps . such contiguous sequence alignment modules represent sequence similarity between the subject and query chromosome sequence in question ( at their respective positional coordinates ) . this pairwise sequence comparison procedure serves as a rapid and robust way to detect duplication relationships . however , because of the use of masked sequences , our method would only yield a poor ( on average 0.1 - 0.5 kb ) resolution for the determination of the precise duplication alignment boundaries . results were classified as either duplications or ' questionable ' results based on sequencing status of the region and the percent sequence similarity between the detected alignments . questionable duplications are results that fall within regions containing draft sequences with > 99.5 % detected sequence identity with another region . we consider these questionable duplications to be involved in potential sequence misassignment errors in the human genome assembly and would require further effort to achieve resolution . detailed information regarding segmental duplications as well as potential sequence misassignment errors identified by our analysis were presented using the generic genome browser . we have also summarized our results in table formats   that include information on size of duplications , chromosomal band locations , level of identity between duplicated copies , sequenced clones ( accession numbers ) and their sequencing status , as well as genes mapped to these regions . in addition , we have plotted the size of each intrachromosomal duplication ( y - axis ) against its chromosome position ( x - axis ) along each chromosome to indicate the intrachromosomal segmental duplication content of each chromosome ( figure 1 ) using the publicly available visualization tool genomepixelizer . results generated from the detection of segmental duplications were subsequently converted into coordinate files as input for display using genomepixelizer . each chromosome snp table , containing annotation regarding ambsnps that have appeared twice in a particular chromosome , were extracted and sorted along with their corresponding chromosomal positions . the number of ambsnps was tabulated along a 10-kb window to produce density plots of ambsnps along the length of each chromosome ( figure 1 ) . we obtained the december 2001 , april 2002 , and june 2002 ( ncbi build 28 , 29 and 30 respectively ) human genome assemblies through the university of california , santa cruz human genome browser . all chromosome sequences were lower - case masked for highly repetitive elements by repeatmasker ( a.f.a . each of the 25 masked chromosome sequences ( including one unmapped chromosome sequence ' chrun ' ) was compared against itself by chromosome - wide blast2   to detect intrachromosomal segmental duplications ( 25 comparisons made ) , as well as pairwise comparisons to each of the other 24 chromosomes to detect interchromosomal segmental duplications ( 600 comparisons made ) . all blast results were subsequently parsed to eliminate low - quality and fragmented alignments under the following criteria : blast results having  90% sequence identity ,  80 bp in length , and with expected value  10 . each blast report was sorted by chromosomal coordinates . all identical hits ( same coordinate alignments ) , including suboptimal blast alignments recognized by multiple , overlapping alignments , as well as mirror hits ( reverse coordinate alignments ) from the blast results of the intrachromosomal set were removed . contiguous alignments separated by a distance of less than 3 kb , then 5 kb , and subsequently 9 kb were joined ( stepwise ) into modules in order to traverse masked repetitive sequences and to overcome breaks in the blast alignments caused by insertions / deletions and sequence gaps . such contiguous sequence alignment modules represent sequence similarity between the subject and query chromosome sequence in question ( at their respective positional coordinates ) . this pairwise sequence comparison procedure serves as a rapid and robust way to detect duplication relationships . however , because of the use of masked sequences , our method would only yield a poor ( on average 0.1 - 0.5 kb ) resolution for the determination of the precise duplication alignment boundaries . results were classified as either duplications or ' questionable ' results based on sequencing status of the region and the percent sequence similarity between the detected alignments . questionable duplications are results that fall within regions containing draft sequences with > 99.5 % detected sequence identity with another region . we consider these questionable duplications to be involved in potential sequence misassignment errors in the human genome assembly and would require further effort to achieve resolution . detailed information regarding segmental duplications as well as potential sequence misassignment errors identified by our analysis were presented using the generic genome browser . we have also summarized our results in table formats   that include information on size of duplications , chromosomal band locations , level of identity between duplicated copies , sequenced clones ( accession numbers ) and their sequencing status , as well as genes mapped to these regions . in addition , we have plotted the size of each intrachromosomal duplication ( y - axis ) against its chromosome position ( x - axis ) along each chromosome to indicate the intrachromosomal segmental duplication content of each chromosome ( figure 1 ) using the publicly available visualization tool genomepixelizer . results generated from the detection of segmental duplications were subsequently converted into coordinate files as input for display using genomepixelizer . each chromosome snp table , containing annotation regarding ambsnps that have appeared twice in a particular chromosome , were extracted and sorted along with their corresponding chromosomal positions . the number of ambsnps was tabulated along a 10-kb window to produce density plots of ambsnps along the length of each chromosome ( figure 1 ) . the following additional data are availiable as a single file with this article : a table describing the relative frequency increase of repeat types at duplicon junctions ( additional data file 1 ) ; a table giving the number of ambiguousgly mapped snps within segmental duplications ( number of psvs ) ( additional data file 1 ) ;   a figure ( additional data file 1 ) showing functional profiling of genes involved in recent whole - gene duplication vs human genome average . this work was supported by the canadian institutes of health research ( cihr ) and genome canada to s.w.s . and x.e . is a senior scientist at the centre de regulaci genmica ( crg ) and a visiting scientist of the hospital for sick children research institute . s.w.s . is a scholar of cihr and international scholar of the howard hughes medical institute . left , graphical views of the paralogous relationships between recent segmental duplications ( graphics produced using genomepixelizer ; each line represents a duplicated module ; coloring scheme , red = 99% to 100% sequence identity , purple = 96% to 98% , green = 93% to 95% , and blue = 90% to 92% ) . middle panel : segmental duplications as detected by blast analysis ( size of duplication in kb plotted against the length of chromosome in mb ) . right panel : ambsnps density plot ( number of ambsnps plotted against the length of chromosome in mb ) . ac121339 is incorrectly mapped to 3q13.13 in the june 2002 human genome assembly as shown by a consensus number of chromosome x sts markers . segmental duplication content of the human genome * previous data on segmental duplications distributed by chromosomes as reported in . comparison of duplications and potential sequence misassignment errors in genome assemblies * all numbers shown in the table are  100 kb . * segmental duplications involved in known genomic disorders and chromosome rearrangements identified by blast and ambsnp analyses this table represents a partial list of all known genomic disorders and chromosome rearrangements . * only the start coordinates ( based on june 2002 assembly ) for duplicons are shown . results from blast analysis with chromosome coordinates and size of duplicon . for several genomic mutations ( williams - beuren syndrome , prader - willi syndrome and angelman syndromes , and digeorge syndrome ) the duplicons shown are incomplete , most of which are composed of several duplication modules . the ' - ' sign indicates that the second duplicon is in the inverse orientation . the number of ambsnps ( ambiguously mapped single - nucleotide polymorphisms ) found within the genomic segment . the ambsnp analysis defines regions containing high densities of contiguous ambsnps . for some of the segmental duplications involved in genomic disorders , the contiguous lengths of ambsnps are much larger than those detected by blast . the specific sizes of the segmental duplications have to be resolved by detailed characterization of the different modules . celera representation : s , both copies found in large ( > 500 kb ) sequence scaffolds ; p , partially hit , single copy found , or less than perfect alignments ; m , missing from large sequence scaffolds , hitting numerous fragments .
rapid computational heuristics have been developed based on blast analysis to detect segmental duplications , as well as regions containing potential sequence misassignments in the human genome assemblies . 
 most of the sequences in the human genome that have undergone recent segmental duplications have now been identified .