snpout4/

4 SNP groups, 3 read groups, mapped with gsnap to cacao3h coding sequences.

SNP data in snp4pub3hcds.txt (snpid, geneid:position, refbase-snpbase)

Rna read data: 
The genotypes are:  CCN51, TSH1188, Pound7 and UF273 type 1.
  Pound7 renamed as pn11..pn16 corresponding with SNPgrp#1 Pound_7 (idtag=po) NOTE: tags pn==po Pound_7
  CNN,TSH renamed as tc01..tc10, correspoding with SNPgrp#2,3 ccn51 (idtag=cc), tsh1188 (idtag=ts)
  UF273_Type1 renamed as uf18..uf21, corresponding with SNPgrp#4 UF273_Type1 (idtag=uf)

map2cds/
GSnap mapping results in map2cds/ include all mapped reads, in gsnap text output format with
 snps: ids found in reads.  
Subset of only those reads with snps: are extracted into snp4o3pn_snpout.tar.gz, ..
 files (per read group, lane).  These are analyzed for relation to gene cds position in tables.

snp4cdstab/  
  tables per read-group, lane, of genes with snp changes, in this format:
GeneID__________        bCDS    cdn     scod    qcod    dAA     SNPid   SNPgrp
Thecc1EG019914t1        558     3       GCc     GCA     A=A     s4b25709437     cc,po,uf
Thecc1EG019914t1        567     3       AGt     AGC     S=S     s4b25709446     cc,po,ts,uf
Thecc1EG029926t1        1698    3       TTg     TTA     L=L     s6b24968307     po,uf

bCDS= base position in CDS, cdn=codon1,2,3 scod,qcod = source,query codon, dAA= amino change,
SNPid= scaffold-base position, SNPgrp = groups at position
Nr = number of reads, for summary tables.

snp4cds2tab/ 
  tables of same as above, with restriction of 2 snp of same group found per read tabulated.

Summary tables per genotype:
snp4o3uf.snpsum.tab, pn, tc: read counts for each gene-base with snp
snp4o3uf.snp2sum.tab, pn, tc: 2-snp read counts
subsets: -sc4m2 = 508 genes in scaffold4:1-2M range
         _gexregion = gene ids Thecc1EG01680.t1|Thecc1EG01679.t1 including Gex1a,b,c in scaf4

snp4_gexregion.snp2.tab
GeneID__________        bCDS    Nr      cdn     scod    qcod    dAA     SNPid   SNPgrp
==== snp4o3pn.snp2sum_sc4m2.tab ==========  All Pound7 reads with 2+snp per read
Thecc1EG016791t1        179     16      2       CaT     CGT     H>R     s4b203138       po,ts
Thecc1EG016791t1        192     16      3       GCg     GCC     A=A     s4b203151       po,ts,uf
                        ^2pos  ^16 read each                               snpgrps po,ts ^^ share 2-snp
Thecc1EG016799t1        626     1       2       AgT     ATT     S>I     s4b246166       po,ts
Thecc1EG016799t1        679     1       1       tGT     AGT     C>S     s4b246113       po
Thecc1EG016799t1        765     1       3       ATa     ATG     I>M     s4b246027       po,ts,uf
Thecc1EG016799t1        771     1       3       AAt     AAC     N=N     s4b246021       ts
Thecc1EG016799t1        777     1       3       CAa     CAT     Q>H     s4b246015       ts
Thecc1EG016799t1        797     1       2       AtG     ACG     M>T     s4b245995       po,ts
Thecc1EG016799t1        826     1       1       cAT     TAT     H>Y     s4b245966       po
Thecc1EG016799t1        854     2       2       GcT     GTT     A>V     s4b245938       ts
Thecc1EG016799t1        860     2       2       TcA     TTA     S>L     s4b245932       po,ts
Thecc1EG016799t1        878     2       2       AgC     ACC     S>T     s4b245914       po
Thecc1EG016799t1        1066    1       1       gTG     CTG     V>L     s4b245638       cc,po,uf
Thecc1EG016799t1        1073    1       2       CtG     CAG     L>Q     s4b245631       po
Thecc1EG016799t1        1088    1       2       GaA     GGA     E>G     s4b245616       po
Thecc1EG016799t1        1096    1       1       cAA     GAA     Q>E     s4b245608       po
Thecc1EG016799t1        1114    1       1       gAA     AAA     E>K     s4b245590       po
Thecc1EG016799t1        1348    1       1       gCT     ACT     A>T     s4b245281       ts
Thecc1EG016799t1        1393    1       1       tTA     GTA     L>V     s4b245103       ts
...