# cacao3 = cacao v1.1asm Rna-seq 

Chr 7 has 50% fewer rna reads than other chromosomes.
Another oddity of chr7, along w/ 2x more non-align spans.
Also 7 has only 70% as many introns (proportional to # reads)

There may also be an EST deficit on Chr 7, which has lowest 
EST read count also:
  sc6.longfa 558854
  sc7.longfa 316387  0.65 s7/s8
  sc8.longfa 486875

Rna read group proportions for Chr 7 / Chr 8 (8 slightly smaller than 7)
Do read groups with 1.0 proportion explain any of this?
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solexa_transcriptome/
1_SCA6.353+372+408.1 scaffolds 7/8	0.89	484163 / 540265
2_U48.353+372+408.1 scaffolds 7/8	1.28	1260821 / 980286
3_GU255_P.353+372+408.1 scaffolds 7/8	0.83	1058823 / 1262109
4_IMC51.353+372+408.1 scaffolds 7/8	0.82	941823 / 1137168
5_AMAZ_15_15.353+372+408.1 scaffolds 7/8	0.61	695669 / 1134758
COC3335.353+372+408.1 scaffolds 7/8	0.58	528275 / 906890
CRIOLLO_13.353+372+408.1 scaffolds 7/8	0.83	699202 / 840122
EBC_148_leaf_1.462+471+477_subset2.1 scaffolds 7/8	0.93	676861 / 720862
NAP_30.353+372+408.1 scaffolds 7/8	1.06	503445 / 472996
PA_120_B.353+372+408.1 scaffolds 7/8	1.04	1007095 / 962096
PA_150.353+372+408.1 scaffolds 7/8	0.6	540209 / 899423
Pound_5C_a.421.1 scaffolds 7/8	1.1	1343453 / 1211074
Pound_7_2.421.1 scaffolds 7/8	0.82	345005 / 417893
U26.353+372+408.1 scaffolds 7/8	1.03	788840 / 759315

cgb/
cgb_ca10_1 scaffolds 7/8	0.69	688706 / 993830
cgb_ca1_1 scaffolds 7/8	0.57	726468 / 1262210
cgb_ca2_1 scaffolds 7/8	0.56	727584 / 1280131
cgb_ca3_1-i0 scaffolds 7/8	0.55	1897086 / 3390920
cgb_ca3_1-i1 scaffolds 7/8	0.55	1888019 / 3389716
cgb_ca3_1-i2 scaffolds 7/8	0.55	1893202 / 3386647
cgb_ca3_1-i3 scaffolds 7/8	0.55	1891311 / 3390338
cgb_ca4_1 scaffolds 7/8	0.54	742162 / 1349575
cgb_ca5_1 scaffolds 7/8	0.66	852695 / 1280251
cgb_ca6_1 scaffolds 7/8	0.62	540919 / 865234
cgb_ca7_1 scaffolds 7/8	0.58	635927 / 1081276
cgb_ca8_1 scaffolds 7/8	0.68	844580 / 1226010
cgb_ca9_1 scaffolds 7/8	0.66	848752 / 1275904

ncgr/
ncgr090511_1_1-mars11 scaffolds 7/8	0.5	653630 / 1300633
ncgr090511_2_1-mars11 scaffolds 7/8	0.51	1093362 / 2139264
ncgr090609_1_1-mars11 scaffolds 7/8	0.9	471591 / 523594
ncgr090609_2_1-mars11 scaffolds 7/8	1.29	1236373 / 951255
ncgr090609_3_1-mars11 scaffolds 7/8	0.83	1093869 / 1309065
ncgr090609_4_1-mars11 scaffolds 7/8	0.83	920677 / 1106338
ncgr090609_6_1-mars11 scaffolds 7/8	0.61	961002 / 1561963
ncgr090714_2_1-mars11 scaffolds 7/8	0.58	644184 / 1104413
ncgr090714_3_1-mars11 scaffolds 7/8	1.07	581531 / 541847
ncgr090714_4_1-mars11 scaffolds 7/8	0.83	662102 / 797394
ncgr090714_6_1-mars11 scaffolds 7/8	1.04	970456 / 931972
ncgr090714_7_1-mars11 scaffolds 7/8	0.6	523665 / 872478
ncgr090714_8_1-mars11 scaffolds 7/8	1.04	809353 / 776888
ncgr090728_7_1-mars11 scaffolds 7/8	1.12	1775288 / 1575996
ncgr090728_8_1-mars11 scaffolds 7/8	0.84	542156 / 639811
ncgr090922_7_1-mars11 scaffolds 7/8	0.54	387717 / 717147
ncgr090922_8_1-mars11 scaffolds 7/8	0.52	576271 / 1100181
ncgr090929_1_1-mars11 scaffolds 7/8	0.56	484743 / 865468
ncgr090929_2_1-mars11 scaffolds 7/8	0.55	1350380 / 2425709
ncgr090929_4_1-mars11 scaffolds 7/8	0.54	1078800 / 1975973
ncgr090929_7_1-mars11 scaffolds 7/8	0.59	631009 / 1063126
ncgr090929_8_1-mars11 scaffolds 7/8	0.59	664433 / 1111887
ncgr091005_1_1-mars11 scaffolds 7/8	0.57	697732 / 1215315
ncgr091005_2_1-mars11 scaffolds 7/8	0.68	828804 / 1214225
ncgr091005_3_1-mars11 scaffolds 7/8	0.63	302115 / 472929
ncgr091005_4_1-mars11 scaffolds 7/8	0.66	1148031 / 1714319
ncgr091005_6_1-mars11 scaffolds 7/8	0.94	1413700 / 1498697
#.. failed map runs, need redo
# ncgr090929_3_1-mars11.bam.fail   
# ncgr090929_6_1-mars11.bam.fail