euGenes/Arthropods About EvidentialGene BLAST Gene Search Maps Data DroSpeGe
Arthropod EST map errors x Assembly size

Arthropod EST map errors by Assembly unit size

ESTs for Arthropod species here are measured for errors mapping to genome assemblies. The density of errors is plotted against assembly unit bins from large to small. Scaffold bins have approximately the same base size, with small scaffolds in higher bins (14..25). This tests if small scaffolds have a higher portion of errors (H1) versus same distribution (null hypothesis). Small scaffolds tend to have lower assembly coverage, more missing and mis-called bases.

Errors measured (red lines) versus uniquely, perfectly mapped ESTs (black lines):
1. ESTs with duplicate locations (GMAP align with > 95% identity in 2+ locations)
2. EST mapping failures (poor align < 90% identity)
Species: Pea Aphid, Daphnia pulex waterflea, Nasonia vit. jewel wasp, Ixodes scap. tick,
fruit flies Drosophila erecta, Drosophila mojavensis, Drosophila grimshawi

Don Gilbert, Nov. 2009

EST low Identity Errors

            OK Error  pError
aphid   136041 21869  0.138
bombyx  209121 30964  0.129
daphnia 114128 31450  0.216
ixodes  130902 54881  0.295
nasonia 147382 20441  0.122 
     

EST Duplicate locations

          One   Diff  Split  Same   Err  p.Diff  p.Split  p.Same   p.Err
aphid   132559 10955   1535   729 14698  0.0683  0.00957  0.00454  0.0916
bombyx  209897 16456   1578  3516  7764  0.0688  0.00660  0.01470+ 0.0325
daphnia 115809  6112    462  1594 24820  0.0411  0.00310  0.01071+ 0.1668+
ixodes  149662  9914   5388   630 20614  0.0532  0.02894+ 0.00338  0.1107
nasvit  156288  3499   1698   197 11268  0.0202  0.00982  0.00114  0.0652 
Duplicate key: One= EST has one unique location; Diff= EST duplicates on 2 scaffolds; Split= EST is split between scaffolds; Same= EST duplicates on same scaffold; Err= EST fail to map (low or zero identity)

EST Duplicates (red) by Scaffold size
Aphid, Bombyx, Daphnia, Ixodes, Nasonia

Scaffold sizes (X axis) are from Large (left) to small (right).

EST low Identity Errors (red) by Scaffold size
Aphid, Bombyx, Daphnia, Ixodes, Nasonia

Scaffold sizes (X axis) are from Large (left) to small (right).

      Name                               Last modified       Size  Description

[DIR] Parent Directory 05-Dec-2009 19:44 - [IMG] aphid.dup.dens.png 05-Dec-2009 21:08 55k [IMG] aphid.failest.dens.png 03-Dec-2009 21:23 58k [TXT] arthropod-estmap-assemblysize.html 06-Dec-2009 17:57 3k [IMG] bombyx.dup.dens.png 05-Dec-2009 21:09 59k [IMG] bombyx.failest.dens.png 03-Dec-2009 21:23 62k [IMG] daphnia.dup.dens.png 05-Dec-2009 21:09 62k [IMG] daphnia.failest.dens.png 03-Dec-2009 21:23 60k [DIR] densplots/ 06-Dec-2009 18:26 - [DIR] est_map_data/ 06-Dec-2009 21:39 - [TXT] estmaperr.txt 05-Dec-2009 18:53 17k [IMG] ixodes.dup.dens.png 05-Dec-2009 21:09 62k [IMG] ixodes.failest.dens.png 03-Dec-2009 21:23 61k [IMG] nasvit.dup.dens.png 05-Dec-2009 21:09 61k [IMG] nasvit.failest.dens.png 03-Dec-2009 21:23 66k


Developed at the Genome Informatics Lab of Indiana University Biology Department