This track shows the alignments of recently sequenced Ebola samples to the $Organism reference sequence G3683/KM034562.1.
Pairwise alignments of each species to the $Organism genome are displayed as a series of colored blocks indicating the functional effect of polymorphisms (in pack mode), or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, percent identity of the whole alignments is shown in grayscale using darker values to indicate higher levels of identity.
In pack mode, regions that align with 100% identity are not shown. When there is not 100% percent identity, blocks of four colors are drawn.
Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults).
To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.
When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the $Organism sequence at those alignment positions relative to the longest non-$Organism sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".
Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:
Ebola sequences are found NCBI Nucleotide with the search term: (ebola[title] or ebolavirus[title]) and genome
The sequences are aligned to the reference sequence with an ordinary Smith-Waterman alignment command faAlign from the 'kent' source utilities.
psl score of alignments | |||||||||
---|---|---|---|---|---|---|---|---|---|
reference | chrStart | chrEnd | query | query size | score | identity | collection date | country | isolate |
KM034562v1 | 0 | 18957 | KP096422v1 | 18958 | 18941 | 100.00 | Mar-2014 | Guinea | H.sapiens-tc/GIN/14/WPG-C15 |
KM034562v1 | 0 | 18957 | KP178538v1 | 18958 | 18941 | 100.00 | 03-Aug-2014 | Liberia | Ebola virus/H.sapiens-wt/LBR/2014/Makona-201403007 |
KM034562v1 | 0 | 18957 | KP342330v1 | 18958 | 18941 | 100.00 | Oct-2014 | Guinea: Conacry | H.sapiens-wt/GIN/2014/Conacry-192 |
KM034562v1 | 0 | 18957 | KP096421v1 | 18958 | 18937 | 100.00 | Mar-2014 | Guinea | H.sapiens-tc/GIN/14/WPG-C07 |
KM034562v1 | 0 | 18957 | KP096420v1 | 18958 | 18935 | 100.00 | Mar-2014 | Guinea | H.sapiens-tc/GIN/14/WPG-C05 |
KM034562v1 | 0 | 18957 | KP260799v1 | 18958 | 18933 | 100.00 | 2014 | Mali | Ebola virus H.sapiens/MLI/14/Manoka-Mali-DPR1 |
KM034562v1 | 1 | 18957 | KP184503v1 | 18957 | 18932 | 100.00 | 25-Aug-2014 | UK: GB | Ebola virus /H.sapiens-tc/GBR/2014/Makona-UK1.1 |
KM034562v1 | 0 | 18957 | KP260800v1 | 18958 | 18927 | 100.00 | 2014 | Mali | Ebola virus H.sapiens/MLI/14/Manoka-Mali-DPR2 |
KM034562v1 | 0 | 18957 | KP260801v1 | 18958 | 18925 | 100.00 | 2014 | Mali | Ebola virus H.sapiens/MLI/14/Manoka-Mali-DPR3 |
KM034562v1 | 0 | 18957 | KP260802v1 | 18958 | 18923 | 100.00 | 2014 | Mali | Ebola virus H.sapiens/MLI/14/Manoka-Mali-DPR4 |
KM034562v1 | 36 | 18956 | KP120616v1 | 18920 | 18898 | 100.00 | 25-Aug-2014 | UK: GB | H.sapiens-wt/GBR/2014/ManoRiver-UK1 |
KM034562v1 | 29 | 18957 | KP658432v1 | 18929 | 18894 | 100.00 | 29-Dec-2014 | UK: GB | Ebola virus/H.sapiens-wt/GBR/2014/Makona-UK2 |
KM034562v1 | 3 | 18956 | KM519951v1 | 18953 | 17741 | 96.90 | 2014 | DRC | Ebola virus/H.sap-wt/COD/2014/Boende-Lokolia |
KM034562v1 | 16 | 18955 | KP271018v1 | 18941 | 17713 | 96.80 | 20-Aug-2014 | DRC | Ebola virus/H.sapiens/COD/2014/Lomela-Lokolia16 |
KM034562v1 | 45 | 18841 | KM655246v1 | 18797 | 17682 | 97.10 | 1976 | Zaire | H.sapiens-tc/COD/1976/Yambuku-Ecran |
KM034562v1 | 53 | 18914 | KP271020v1 | 18861 | 17635 | 96.80 | 20-Aug-2014 | DRC | Ebola virus/H.sapiens/COD/2014/Lomela-Lokolia19 |
KM034562v1 | 176 | 18936 | KP271019v1 | 18760 | 15340 | 96.70 | 20-Aug-2014 | DRC | Ebola virus/H.sapiens/COD/2014/Lomela-Lokolia17 |
KM034562v1 | 4 | 18336 | NC_016144v1 | 18927 | 3194 | 58.90 | 2003 | Spain | Lloviu virus |