Index of /EvidentialGene/arthropods/nasoniawasp/asm2map

 Name                             Last modified       Size  

 Parent Directory                 25-Mar-2019 14:24      -  
 nasvit21asm.fa.count             16-Aug-2013 14:00   297k  
 nasvit21asm.fa.gz                21-Feb-2013 16:29  79.5M  
 nvitevg11_nasv21a.align.tab.gz   21-Feb-2013 21:47   907k  
 nvitevg11_nasv21a.gmap.gff.gz    21-Feb-2013 21:48   9.9M  
 nvitevg11_nasv21a.misalign95.tab 21-Feb-2013 21:49   131k  

Nasvit2 genes mapped on to Nasonia vitrip. genome assembly in 
GenBank  Nvit_2.1, released on Nov 28, 2012.
http://www.ncbi.nlm.nih.gov/assembly/GCA_000002325.2/

 297K Aug 16 14:00 nasvit21asm.fa.count    : Nvit_2.1 genome asm scaffold base count table
  79M Feb 21 16:29 nasvit21asm.fa.gz       : Nvit_2.1 genome asm scaffolds 

  60M Feb 21 21:48 nvitevg11_nasv21a.gmap.gff   : gene transcripts mapped to nv21 assembly 
           EvidentialGene/nasonia/genes/nvit2_evigenes_pub11u.tr.gz 
 3.6M Feb 21 21:47 nvitevg11_nasv21a.align.tab  : per gene table of map locations, quality
 131K Feb 21 21:49 nvitevg11_nasv21a.misalign95.tab  : 1597 mis-mapping genes (<95% aligned)

Example align.tab :
GeneID  gespan  geor    QueryID quspan  match   qlen    cov     pid     path    indels  cdsindel
... no aligns
NOPATH  1-69    .       Nasvi2EG014342bt1       1-69    0       99      0       1       0/0     0       631
NOPATH  1-69    .       Nasvi2EG020258t1        1-69    0       99      0       1       0/0     0       273
.... perfect aligns
nvit21GL340867_2        44502-56945     +       Nasvi2EG000001t1        1-2689  2689    2689    100.0   100.0   0       0       0
nvit21GL340867_2        306-123702      +       Nasvi2EG000002t1        1-3462  3462    3462    100.0   100.0   0       0       0
nvit21GL340867_2        425199-463600   -       Nasvi2EG000025t4        1-3796  3796    3796    100.0   100.0   0
... misaligns
nvit21AAZX01000634_1    5344-6815       -       Nasvi2EG024849t1        1080-2405       1266    3781    35.1    95.0    1/2     39/7    39
nvit21AAZX01000634_1    6059-7433       +       Nasvi2EG035300t1        1087-2161       1075    2401    44.8    100.0   0       0       0
nvit21AAZX01002207_1    3248-10550      +       Nasvi2EG036090t1        285-746 453     746     61.9    100.0   0       0       0

 key: GeneID here is scaffold ID; gespan = mRNA span on scaffold, geor = orientation on scaf.
      QueryID = mRNA ID; quspan = mRNA aligned span, match = bases aligned, qlen = mRNA length,
      cov = percent align coverage, pid = percent identity, path = number of locations/paths/breaks,
      indels, cdsindel = count of insert/del in mapping.

Example genes.gff
  scaffold nvit21GL340867_2 ==  http://www.ncbi.nlm.nih.gov/nuccore/GL340867.2

nvit21GL340867_2        nv1gene11u      mRNA    425199  463600  100     -       .       ID=Nasvi2EG000025t4;Target
=Nasvi2EG000025t4 1 3796;aalen=666;cov=100.0;match=3796;nexon=9;pid=100.0;qlen=3796
nvit21GL340867_2        nv1gene11u      exon    463353  463600  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 1 248;ix=1
nvit21GL340867_2        nv1gene11u      exon    461095  461291  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 249 445;ix=2
nvit21GL340867_2        nv1gene11u      exon    430893  430982  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 446 535;ix=3
nvit21GL340867_2        nv1gene11u      exon    430150  430330  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 536 716;ix=4
nvit21GL340867_2        nv1gene11u      exon    429107  429709  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 717 1319;ix=5
nvit21GL340867_2        nv1gene11u      CDS     429107  429565  100     -       .       Parent=Nasvi2EG000025t4
nvit21GL340867_2        nv1gene11u      exon    427643  428157  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 1320 1834;ix=6
nvit21GL340867_2        nv1gene11u      CDS     427643  428157  100     -       .       Parent=Nasvi2EG000025t4
nvit21GL340867_2        nv1gene11u      exon    427063  427522  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 1835 2294;ix=7
nvit21GL340867_2        nv1gene11u      CDS     427063  427522  100     -       .       Parent=Nasvi2EG000025t4
nvit21GL340867_2        nv1gene11u      exon    426595  426971  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 2295 2671;ix=8
nvit21GL340867_2        nv1gene11u      CDS     426595  426971  100     -       .       Parent=Nasvi2EG000025t4
nvit21GL340867_2        nv1gene11u      exon    425199  426323  100     -       .       Parent=Nasvi2EG000025t4;Ta
rget=Nasvi2EG000025t4 2672 3796;ix=9
nvit21GL340867_2        nv1gene11u      CDS     426134  426323  100     -       .       Parent=Nasvi2EG000025t4