Help with the HuRef Browser

This page covers the help topics listed below. For assistance with a topic not covered on this page please send e-mail to hurefhelp@jcvi.org.

getting started

On the HuRef browser home page there are two ways to select an initial region of interest to view in the browser, as indicated in the following image:
HuRef entry page
The two options depicted here are:
  1. Enter a search term into the "Search" text entry box at the top of the page and then either press "Enter" or click on the "Search" button (see using the search widget for more detailed instrutions on using this approach).
  2. Click on one of the cytogenetic bands in the "Browse By Karyotype" section. (Holding the mouse pointer over a band will display its name.)
In either case the main browser application will launch and attempt to display the selected region of interest in the NCBI 36.1 human consensus sequence. If that region of the NCBI 36.1 sequence can be mapped to a region in the HuRef diploid genome via the assembly to assembly comparison (ATAC), then the corresponding HuRef contigs and/or scaffolds--and their associated annotations--will also be shown, as will the mapping between the NCBI 36.1 reference sequence and the HuRef contigs and scaffolds.

the main application layout

The following image highlights the principle components of the main HuRef browser application: HuRef browser main application layout

1. status bar

Status and error messages appear in this area of the browser window when appropriate, for example, when a search or navigation request is submitted.

2.search widget

The search widget, which appears both at the top of the main browser interface and also on the browser home page, consists of an area into which text may be entered, along with a button labeled "Search":
Search widget
The search widget allows you to find and display a single specific feature or region, and it accepts several different types of feature and region identifiers. To use the widget, enter a search term into the text area and then either press Enter on the keyboard or click on the "Search" button. Here are some examples of valid search terms that may be entered into the widget:
  • A chromosome or sequence id followed by a start position and region length e.g., "chr19:450000+100000" to display the region from 450000-550000 on chromosome 19.
  • A dbSNP id e.g., "rs2691286"
  • An Ensembl annotation identifer e.g., "ENSG00000104783"
  • A gene name, e.g. "KLKB1", optionally followed by the amount of flanking sequence to display e.g., "KLKB1^2000"

3. navigation bar

At the top right of the browser window there are several buttons that can be used to navigate relative to the currently displayed region:
HuRef navigation bar
  • Zoom In: narrows the displayed region by the indicated amount
  • Zoom Out: widens the displayed region by the indicated amount
  • Pan (<, >): Moves the displayed region to the left or right by a small amount
  • Pan (<<, >>): Moves the displayed region to the left or right by a large amount

4. NCBI assembly view

This area of the browser display shows a reference chromosomal region from the NCBI sequence assembly (at the top of the area, along with a scale icon showing the region covered by the display.) Beneath the scale indicator is a set of one or more annotation tracks showing the locations of various types of annotations that have been localized to the NCBI assembly. See adding, removing, and reordering annotation tracks for information on changing and reordering the annotation tracks displayed in this area. For more information on the data shown by a particular track simply click on the track title immediately above each track.

5. NCBI-HuRef Assembly-to-Assembly Comparison (ATAC) view

This area of the browser display shows the mapping (as computed by the Assembly-to-Assembly Comparison tool, ATAC), from the reference NCBI chromosome region currently displayed in the NCBI assembly view, to those HuRef contigs and scaffolds (depicted as colored rectangles below the NCBI reference chromosome) mapped by ATAC. Shaded lines drawn between the reference chromosome and the HuRef contigs and scaffolds indicate the matching regions (corresponding to ATAC "match" features.) To select a HuRef contig or scaffold to display in the HuRef assembly view simply click on it in the ATAC view. (Clicking on the NCBI reference chromosome will open the Feature Inspector.)

6. HuRef assembly view

This area of the browser display initially shows the region of the HuRef contig or scaffold that has the best match to the reference NCBI chromosome region shown in the NCBI assembly view. The HuRef contig or scaffold that is displayed by default is typically the longest one that appears in the NCBI-HuRef Assembly-to-Assembly Comparison (ATAC) view. At the top of this area the HuRef contig or scaffold id is displayed, below which is a set of one or more annotation tracks showing the locations of various types of annotations that have been localized to the HuRef assembly. See adding, removing, and reordering annotation tracks for information on changing and reordering the annotation tracks displayed in this area. For more information on the data shown by a particular track simply click on the track title immediately above each track. To change the HuRef contig or scaffold displayed in this area, click on an alternate contig or scaffold in the NCBI-HuRef Assembly-to-Assembly Comparison (ATAC) view.

7. data inspection and download tools

A number of tabs at the very bottom of the main browser window provide additional options for displayed and/or downloading data on specific features or sequence regions that appear in the current browser display. With the exception of the first tab (the "Feature Inspector"), all of the tabs display data for the NCBI and/or HuRef sequence regions currently displayed in the NCBI assembly view. This area of the browser page automatically expands vertically (obscuring part of the browser display as it does so) whenever either:
  • The mouse pointer is clicked on a feature in any annotation track, triggering the Feature Inspector tab.
  • Any of the tabs at the bottom of the browser page is clicked on.
The area occupied by the tabbed portion of the page may be adjusted manually by clicking and dragging the line that divides it from the top part of the page. More importantly, clicking a second time on the currently-active tab will minimize the tabbed portion of the page. the Feature Inspector
From left to right, the tabs in this portion of the browser page are:
  • Feature Inspector: Triggered by clicking on any feature in an annotation track. Displays detailed information for each feature, including the sequence coordinates and literal sequence.
  • Seq Alignment: Displays the DNA sequence of each chromosome, contig, scaffold, and sequence read included in the current display, using a tabular layout.
  • GFF Table: Displays the annotations visible in the NCBI assembly view as a GFF-style table (with an option download the table as a standard GFF flat file.)
  • SNP Analysis: Displays detailed SNP allele and flanking sequence information for each HuRef SNP in the current browser display.
  • SNP Evidence: Maps SNPs to reads and read quality values.
  • SNPs in Repeats: Lists SNPs that overlap with repeats.
  • Annotations: List features (i.e., Genes) with OMIM or Gene Ontology links/assignments.

adding, removing, and reordering annotation tracks

Annotations in the browser are grouped into horizontal "tracks", and each track typically contains either a single type of annotation or a small number of related annotation types.

Adding an annotation track:

When the browser is initially launched it displays a default set of annotation tracks. However, additional tracks are available that are not displayed by default. To add one of these tracks to the display, left-click on the pull-down menu labeled "Add/Remove Tracks". This should display the full set of available annotation tracks; those with a check mark displayed next to them are the tracks that appear in the current display. To add a track, find one that does not already have a check mark next to it and click on either the checkbox or the name of the track. After a short pause the requested track should appear as the new top annotation track in the browser.

Removing an annotation track:

There are two ways to remove an annotation track from the current browser display:
  1. Use the same pull-down menu described in "Adding an annotation track" to uncheck, or click on the name of, any track that has a check mark next to it.
  2. Click on the close icon that appears to the left of the name of each annotation track.

Reordering annotation tracks:

To change the vertical position of a track in the browser:
  1. Click on the background of the annotation track (i.e., any part of the track not occupied by an actual annotation).
  2. Drag the track to its new location by moving the mouse. A copy of the track should move with the mouse as it is dragged, and a horizontal black line will indicate where the track will move when the mouse button is released.
  3. Release the mouse button to drop the track into its new location. The browser display should update accordingly.

annotation track descriptions

Annotation track types marked with a "*" (e.g.., "*Gene") are those that appear in the default HuRef browser display. Tracks may be added, removed, and reordered as described above.

*Gene [chromosome]

A gene describes a collection of transcripts.
gene annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays genes from the Ensembl release 41.36c annotation of the NCBI 36.1 assembly of the human genome. Each gene appears as a shaded rectangle with an arrow on either the left or right end to indicate the direction of transcription of the majority of the transcripts in the gene, either 5’ - 3’ (arrow on the right) or 3’ - 5’ (arrow on the left.)

*MRNA [chromosome]

The intermediate molecule between DNA and protein.
mRNA annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays transcripts (ENST features) from the Ensembl release 41.36c annotation of the NCBI 36.1 assembly of the human genome. Each transcript is labeled with both a gene/locus id and also an Ensembl transcript ID. Exons appear as taller shaded areas on the horizontal line that depicts the transcript, and a series of directional arrows on the transcript indicate the intronic sequence and its direction of transcription.

*Haplotype blocks (longest) [chromosome]

These are the haplotype blocks described in Levy et al.
haplotype_block_longest annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays the "longest" haplotype blocks that are highlighted in the supplemental poster that accompanies the Human Diploid Genome publication in PLoS Biology. Note that the longest haplotype blocks are not necessarily those that contain the most variants. Each haplotype block appears as a shaded horizontal rectangle, color-coded to indicate the total number of variants contained in the block:
Number of variants <= 19
Number of variants >= 20, Number of variants <= 49
Number of variants >= 50, Number of variants <= 99
Number of variants >= 100
Each haplotype block is also labeled with the number of variants that it contains (e.g., "Number of variants=28" for a haplotype block with 28 variants) and its overall length (e.g., "length=114049bp"), which is the distance between the first and the last variant in each block. Note that these haplotype blocks contain both heterozygous and homozygous HuRef variants, in addition to dbSNP variants, so the number of heterozygous HuRef variants phased by any given block will typically be less than the reported "Number of variants" value. The individual variants contained within each block are displayed as narrow vertical bars. A grey vertical bar indicates a heterozygous HuRef variant and a black vertical bar indicates either a homozygous HuRef variant or a dbSNP variant.

Haplotype blocks (other) [chromosome]

These are the haplotype blocks described in Levy et al.
haplotype_block_other annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays all haplotype blocks that do not appear in the haplotype_block_longest track. Each haplotype block appears as a shaded horizontal rectangle, color-coded to indicate the total number of variants contained in the block:
Number of variants <= 19
Number of variants >= 20, Number of variants <= 49
Number of variants >= 50, Number of variants <= 99
Number of variants >= 100
Each haplotype block is also labeled with the number of variants that it contains (e.g., "Number of variants=28" for a haplotype block with 28 variants.) and its overall length (e.g., "length=114049bp"), which is the distance between the first and the last variant in each block. Note that these haplotype blocks contain both heterozygous and homozygous HuRef variants, in addition to dbSNP variants, so the number of heterozygous HuRef variants phased by any given block will typically be less than the reported "Number of variants" value. The individual variants contained within each block are displayed as narrow vertical bars. A grey vertical bar indicates a heterozygous HuRef variant and a black vertical bar indicates either a homozygous HuRef variant or a dbSNP variant.

*HuRef SNPs [chromosome]

A heterozygous or homozygous Single Nucleotide Polymorphism (SNP)
HuRef_SNPs annotation track for ENST00000337401
view this region in the browser: ENST00000337401
This track displays two types of single nucleotide polymorphism (SNP). Heterozygous SNPs (circles) are single base differences between the two HuRef haplotypes. Homozygous SNPs (squares) are single base differences between the HuRef sequence (at locations where both haplotypes agree) and the NCBI 36.1 consensus sequence. Non-synonymous variants are shown in pink and synonymous variants are shown in yellow.

*HuRef Indels or Complex Variants [chromosome]

Indels, block substitutions and complex sequence variations
Scale for chr19:450000-550000:1
HuRef_Indels_or_Complex_Variants annotation track for chr19:450000-550000:1
Assembly-to-Assembly (ATAC) view for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays insertions, deletions, and complex variants that have been identified by comparing the two HuRef haplotypes. Complex variants are variants in which multiple adjacent bases differ between the two HuRef haplotypes, typically combining nucleotide changes (SNPs and MNPS) with indels. Heterozygous complex sequence variants are shown using a "dumbell" glyph consisting of two SNP glyphs (e.g., circles) connected by a horizontal line.

*Homozygous Indels [chromosome]

The set of insertions, deletions and inversions that were identified by an analysis of the output of the Assembly-To-Assembly-Comparison (ATAC) program.
Scale for chr8:6138500+30000
Assembly_Comparison_Differences annotation track for chr8:6138500+30000
Assembly-to-Assembly (ATAC) view for chr8:6138500+30000
view this region in the browser: chr8:6138500+30000
This track displays deletions, insertions, and inversions in the HuRef sequence, relative to the NCBI 36.1 human consensus sequence. The two sequences were compared using the ATAC software and differences were identified and classified, using the NCBI sequence as the reference (i.e. an insertion or deletion is an insertion or deletion in the HuRef sequence, relative to NCBI.) Triangles pointing up represent assembly comparison deletions. Triangles pointing down represent assembly comparison insertions and rectangles that contain an elongated "X" mark (the "crossbox" glyph) represent assembly comparison inversions.

*dbSNP variant [chromosome]

Refers to a variant found in dbSNP. Defined as a region of sequence where variation has been observed.
sequence_variant annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays the location (on the NCBI 36.1 human genome assembly) of SNPs in dbSNP. Note that the dbSNP data were obtained from the annotation files downloaded from Ensembl, and that recently added SNPs in dbSNP may not appear in this track. See the about page for a list of the external data release versions--including Ensembl--used in this build of the HuRef browser.

CDS [chromosome]

A contiguous RNA sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
CDS annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays CDS features from the Ensembl release 41.36c annotation of the NCBI 36.1 assembly of the human genome. Each CDS is displayed as a horizontal rectangle with an arrow on either the left or right end to indicate the direction of transcription and translation.

Exon [chromosome]

A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205).
exon annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays exon features from the Ensembl release 41.36c annotation of the NCBI 36.1 assembly of the human genome. Each exon is displayed as a horizontal rectangle with an arrow on either the left or right end to indicate the direction of transcription of the corresponding transcript.

Five prime UTR [chromosome]

A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
five_prime_UTR annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays 5’-UTR features from the Ensembl release 41.36c annotation of the NCBI 36.1 assembly of the human genome. Each UTR is displayed as a horizontal rectangle with an arrow on either the left or right end to indicate the direction of transcription of the corresponding transcript.

Three prime UTR [chromosome]

A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
three_prime_UTR annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays 3’-UTR features from the Ensembl release 41.36c annotation of the NCBI 36.1 assembly of the human genome. Each UTR is displayed as a horizontal rectangle with an arrow on either the left or right end to indicate the direction of transcription of the corresponding transcript.

Tandem repeat [chromosome, contig]

Two or more adjacent copies of a DNA sequence.
tandem_repeat annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays tandem repeats identified by the TRF (Tandem Repeats Finder) software.

Tandem repeat identical [chromosome, contig]


tandem_repeat_identical annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays TRF-identified tandem repeats that are identical in both HuRef and the NCBI 36.1 sequence assembly.

Tandem repeat extension [chromosome, contig]

Extra copy(ies) or an extension of a tandem repeat motif.
tandem_repeat_extension annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays TRF-identified tandem repeats that are extended in HuRef relative to the NCBI 36.1 sequence assembly.

Tandem repeat truncation [chromosome, contig]

A trunctation or fewer copy(ies) of a tandem repeat motif.
tandem_repeat_truncation annotation track for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
This track displays TRF-identified tandem repeats that are truncated in HuRef relative to the NCBI 36.1 sequence assembly.

Assembly comparison translocation [chromosome]


Scale for chr1:83500000+100000
assembly_comparison_translocation annotation track for chr1:83500000+100000
Assembly-to-Assembly (ATAC) view for chr1:83500000+100000
view this region in the browser: chr1:83500000+100000
The ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly. The ATAC output was post-processed to identify cases in which a region in the HuRef sequence aligns to a different chromosome than the regions around it. Such regions are marked as translocations.

Assembly comparison transposition [chromosome]


Scale for chr1:167450000+100000
assembly_comparison_transposition annotation track for chr1:167450000+100000
Assembly-to-Assembly (ATAC) view for chr1:167450000+100000
view this region in the browser: chr1:167450000+100000
The ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly. The ATAC output was post-processed to identify cases in which a region in the HuRef sequence aligns to a different region of the same chromosome that is matched by the regions immediately surrounding it. These regions are marked as transpositions.

Assembly error singleton fills gap [chromosome]


Scale for chr1:1100000+100000
assembly_error_singleton_fills_gap annotation track for chr1:1100000+100000
Assembly-to-Assembly (ATAC) view for chr1:1100000+100000
view this region in the browser: chr1:1100000+100000
This track indicates regions of the NCBI human reference sequence in which:
  1. A large HuRef contig or scaffold aligns to the region but contains a gap (i.e, a stretch of 'N's in the underlying sequence data)
  2. A smaller HuRef contig aligns to the region covered by the gap in the larger contig/scaffold.
  3. The size of the smaller contig is the same as, or almost the same as, the length of the gap in the larger contig.
The most likely explanation for such situations is that the smaller contig should have been incorporated into the assembly of the larger contig or scaffold, but was not, either due to an assembly error or the lack of sufficient evidence (e.g., no shared mate pairs or sequence sequence overlap.)

Putative assembly comparison block substitution [chromosome]


Scale for chr1:17100000+100000
putative_assembly_comparison_block_substitution annotation track for chr1:17100000+100000
Assembly-to-Assembly (ATAC) view for chr1:17100000+100000
view this region in the browser: chr1:17100000+100000
This feature type is used to describe situations in which there is a gap in the ATAC alignment in both the NCBI and HuRef sequences, and the size of the gap in the HuRef contig/scaffold and the size of the gap in the NCBI assembly are similar. For indels >= 1kb, the length of one gap must be less than or equal to 3X the length of the other gap. For smaller indels the maximum length difference is 4X. Regions that meet these criteria are classified as "block substitutions" rather than an insertions or deletions.

Putative assembly comparison deletion [chromosome]

A putative deletion of undetermined zygosity identified by analysis of the mapping of the consensus sequence of HuRef with NCBI chromosomes. The precise location of the deletion is indeterminate, however, an estimated range can be specified.
Scale for chr1:17200000+100000
putative_assembly_comparison_deletion annotation track for chr1:17200000+100000
Assembly-to-Assembly (ATAC) view for chr1:17200000+100000
view this region in the browser: chr1:17200000+100000
This feature type is used to describe situations in which there is a gap in the ATAC alignment in both the NCBI and HuRef sequences, and the size of the gap in HuRef is smaller than the gap in the NCBI sequence. That is, there appears to be a larger region of unaligned sequence in the NCBI assembly (a deletion in HuRef relative to NCBI), but there is also a small region of unaligned sequence in the HuRef contig/scaffold.

Putative assembly comparison insertion [chromosome]

A putative insertion of undetermined zygosity identified by analysis of the mapping of the consensus sequence of HuRef with NCBI chromosomes. The precise point location of the insertion is indeterminate, however, an estimated range can be specified.
Scale for chr1:17500000+100000
putative_assembly_comparison_insertion annotation track for chr1:17500000+100000
Assembly-to-Assembly (ATAC) view for chr1:17500000+100000
view this region in the browser: chr1:17500000+100000
This feature type is used to describe situations in which there is a gap in the ATAC alignment in both the NCBI and HuRef sequences, and the size of the gap in HuRef is larger than the gap in the NCBI sequence. That is, there appears to be a larger region of unaligned sequence in HuRef (an insertion in HuRef relative to NCBI), but there is also a small region of unaligned sequence in the NCBI assembly.

Sequence rearrangement feature [chromosome]


Scale for chr1:11500000+100000
sequence_rearrangement_feature annotation track for chr1:11500000+100000
Assembly-to-Assembly (ATAC) view for chr1:11500000+100000
view this region in the browser: chr1:11500000+100000
This track displays the position of relatively small and localized rearrangments in the HuRef sequence relative to NCBI. More distant rearrangements on the same chromosome will be classified as assembly_comparison_transposition features.

Assembly comparison insertion atac2 [chromosome]


assembly_comparison_insertion_atac2 annotation track for chr1:850000+950000
view this region in the browser: chr1:850000+950000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the assembly_comparison_insertion track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Assembly comparison deletion atac2 [chromosome]


assembly_comparison_deletion_atac2 annotation track for chr1:38900000+100000
view this region in the browser: chr1:38900000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the assembly_comparison_deletion track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Assembly comparison inversion atac2 [chromosome]


assembly_comparison_inversion_atac2 annotation track for chr1:151800000+100000
view this region in the browser: chr1:151800000+100000

Assembly comparison translocation atac2 [chromosome]


assembly_comparison_translocation_atac2 annotation track for chr1:5600000+100000
view this region in the browser: chr1:5600000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the assembly_comparison_translocation track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Assembly comparison transposition atac2 [chromosome]


assembly_comparison_transposition_atac2 annotation track for chr1:173500000+100000
view this region in the browser: chr1:173500000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the assembly_comparison_transposition track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Assembly error singleton fills gap atac2 [chromosome]


assembly_error_singleton_fills_gap_atac2 annotation track for chr1:195000000+100000
view this region in the browser: chr1:195000000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the assembly_error_singleton_fills_gap track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Putative assembly comparison block substitution atac2 [chromosome]


putative_assembly_comparison_block_substitution_atac2 annotation track for chr1:87700000+100000
view this region in the browser: chr1:87700000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the putative_assembly_comparison_block_substitution track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Putative assembly comparison deletion atac2 [chromosome]


putative_assembly_comparison_deletion_atac2 annotation track for chr1:13000000+100000
view this region in the browser: chr1:13000000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the putative_assembly_comparison_deletion track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

Putative assembly comparison insertion atac2 [chromosome]


putative_assembly_comparison_insertion_atac2 annotation track for chr1:190700000+100000
view this region in the browser: chr1:190700000+100000
After the ATAC (Assembly-to-Assembly Comparison) software was used to compare the HuRef sequence with the NCBI 36.1 sequence assembly, the software was run a second time, but excluding from consideration all HuRef contigs and scaffolds that had been mapped in the first run. The results of this second alignment run are referred to as the ATAC2 results to distinguish them from the results of the first run. The ATAC2 results were subjected to the same analyses as the ATAC results, and annotation tracks that classify the various types of insertions, deletions, and translocations were created in the same way. This annotation track is therefore the same as the putative_assembly_comparison_insertion track, but for the second (ATAC2) alignment run, not the first (ATAC). However, please note that the ATAC2-aligned HuRef contigs and scaffolds are not shown directly in the browser; the assembly to assembly comparison view shows only the first ATAC run.

ATAC run [chromosome]


Scale for chr19:450000-550000:1
match annotation track for chr19:450000-550000:1
Assembly-to-Assembly (ATAC) view for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
An ATAC run between the HuRef consensus sequence and the NCBI 36.1 human genome assembly.

ATAC match [chromosome]


Scale for chr19:450000-550000:1
partial_scaffold annotation track for chr19:450000-550000:1
Assembly-to-Assembly (ATAC) view for chr19:450000-550000:1
view this region in the browser: chr19:450000-550000:1
An ATAC match between the HuRef consensus sequence and the NCBI 36.1 human genome assembly.

*Read pair satisfied [contig]


read_pair_satisfied annotation track for 1103279181064:207263-300000
view this region in the browser: 1103279181064:207263-300000
A mated pair of reads, the distance between which in the HuRef assembly is less than or equal to 3 standard deviations larger or smaller than the mean expected insert size for the library from which they were sequenced.

Read pair too close [contig]


read_pair_too_close annotation track for 1103279181064:207263-300000
view this region in the browser: 1103279181064:207263-300000
A mated pair of reads, the distance between which in the HuRef assembly is more than 3 standard deviations smaller than the mean expected insert size for the library from which they were sequenced.

Read pair too far [contig]


read_pair_too_far annotation track for 1103279181064:207263-300000
view this region in the browser: 1103279181064:207263-300000
A mated pair of reads, the distance between which in the HuRef assembly is more than 3 standard deviations larger than the mean expected insert size for the library from which they were sequenced.

Read pair externally mated [contig]


read_pair_externally_mated annotation track for 1103279181064:207263-300000
view this region in the browser: 1103279181064:207263-300000
A read whose mate is in a different contig or scaffold.

Read pair unassembled [contig]


read_pair_unassembled annotation track for 1103279181064:207263-300000
view this region in the browser: 1103279181064:207263-300000
A read whose mate was not assembled into any contig or scaffold (i.e., it was either unsequenced, or can be found only in a sequence read or region of a sequence read that was not assembled with anything else.)

Heterozygous SNP [contig]

A heterozyous sequence variation identified by analysis of the assembly sequence multialignment.
heterozygous_SNP annotation track for 1103279188415:47381949-47414212
view this region in the browser: 1103279188415:47381949-47414212
A single nucleotide polymorphism that exhibits two distinct alleles in the HuRef sequence (i.e., the maternal and paternal alleles differ in the diploid genome sequence.)

Heterozygous MNP [contig]

A heterozyous Multiple Nucleotide Polymorphism
heterozygous_MNP annotation track for 1103279188415:47381949-47414212
view this region in the browser: 1103279188415:47381949-47414212
A multiple nucleotide polymorphism that exhibits two distinct alleles in the HuRef sequence (i.e., the maternal and paternal alleles differ in the diploid genome sequence.)

Heterozygous insertion [contig]

A heterozyous insertion identified by analysis of the assembly sequence multialignment.
Assembly-to-Assembly (ATAC) view for 1103279188415:47381949-47414212
Scale for 1103279188415:47381949-47414212
heterozygous_insertion annotation track for 1103279188415:47381949-47414212
view this region in the browser: 1103279188415:47381949-47414212
An insertion detected in the HuRef variant allele relative to the consensus allele (based on the aligned reads in the sequence assembly for the displayed contig or scaffold.)

Heterozygous deletion [contig]

A heterozyous deletion identified by analysis of the assembly sequence multialignment.
Assembly-to-Assembly (ATAC) view for 1103279188415:47381949-47414212
Scale for 1103279188415:47381949-47414212
heterozygous_deletion annotation track for 1103279188415:47381949-47414212
view this region in the browser: 1103279188415:47381949-47414212
A deletion detected in the HuRef variant allele relative to the consensus allele (based on the aligned reads in the sequence assembly for the displayed contig or scaffold.)

Heterozygous mixed sequence variant [contig]

A heterozyzygous mixed sequence variant is typically a block substitution containing gap characters in either allele
Assembly-to-Assembly (ATAC) view for 1103279188415:47381949-47414212
Scale for 1103279188415:47381949-47414212
heterozygous_mixed_sequence_variant annotation track for 1103279188415:47381949-47414212
view this region in the browser: 1103279188415:47381949-47414212
A combination of 2 or more contiguous SNPs and indels detected in one HuRef contig or scaffold relative to the other.

Homozygous SNP [contig]

A homozygous Single Nucleotide Polymorphism identified by comparing the consensus sequences of two or more assemblies.
homozygous_SNP annotation track for 1103279188415:47381949-47414212
view this region in the browser: 1103279188415:47381949-47414212
A single nucleotide polymorphism (SNP) that does not appear to be heterozygous in the HuRef sequence (but which has been identified as a SNP either in dbSNP or in a direct comparison of the HuRef sequence to the NCBI consensus sequence.)

Homozygous MNP [contig]

A homozygous Multiple Nucleotide Polymorphism identified by comparing the consensus sequences of two or more assemblies.
homozygous_MNP annotation track for 1103279187391:750000+100000
view this region in the browser: 1103279187391:750000+100000
A multiple nucleotide polymorphism (MNP) that does not appear to be heterozygous in the HuRef sequence (but which has been identified as a SNP either in dbSNP or in a direct comparison of the HuRef sequence to the NCBI consensus sequence.)

contact us

Please contact us with questions or comments via hurefhelp@jcvi.org.