http://server7.eugenes.org:8091/cacao/genes10/rnas/snprna/ ------------------------------------ snp4o3{pn,tc,uf}.snp2cds.sum tables counts of all reads mapping to a genomic SNP position in the gene coding sequences. SNP positions with no read changes are included. Separate files for 3 transcript read sources: tc = tsh1188+ccn51 groups, pn = Pound_7 group, uf = UF273_Type1 group Filtering removed rare changes: filter1: only changes found in >=2 lanes of reads (for 7 lanes x 4..10 subgroups per read group) filter2: report only Nrd >= 25% of maximum Nrd per postion, in cases of 2+ read types found per position 3 transcript read groups, mapped with gsnap to cacao3h coding sequences as per snpout4/ The genotypes are: CCN51, TSH1188 (combined as 'tc'), Pound7 (pn) and UF273 type 1 (uf). 5 genomic SNP groups, in snp5pub3hcdsa.txt, updated from snpout4: ccn51 (cc) Criollo_13 (cr) Pound_7 (po) tsh1188 (ts) UF273_Type1 (uf) Columns in snp2cds.sum tables: GeneID of cacao pub3h gene set bCDS base offset into CDS sequence Nrd number of reads Cdn codon position of reads (from bCDS) Gcdn genomic codon Tcdn transcript codon. Most are same as all non-changed reads are included dAA difference in amino SNPid genomic location of SNP (scaffold, base) SNPgrp group contributing SNP at position, UPPER-CASE group means that SNP base is found in transcript lower-case group means that SNP base is not in transcript Example gene Thecc1EG016792t1 Pound7 reads snp4o3pn.snp2cds.sum GeneID__________ bCDS Nrd Cdn Gcdn Tcdn dAA SNPid SNPgrp Thecc1EG016792t1 1302 53 3 ACG ACG T=T s4b207430 cr,po,ts Thecc1EG016792t1 1302 48 3 ACg ACA T=T s4b207430 CR,PO,TS + silent 48/101 reads Thecc1EG016792t1 1150 68 1 TGG TGG W=W s4b210547 CC Thecc1EG016792t1 1147 61 1 aTG CTG M>L s4b210550 CR,PO,TS,UF + change 61/61 Thecc1EG016792t1 1076 22 2 ACA ACA T=T s4b210621 cr Thecc1EG016792t1 1011 8 3 GAt GAG D>E s4b210686 PO,TS + change 8/11 Thecc1EG016792t1 1011 3 3 GAT GAT D=D s4b210686 po,ts Thecc1EG016792t1 825 29 3 AGC AGC S=S s4b211937 cc Thecc1EG016792t1 569 16 2 GgA GAA G>E s4b212193 CR,PO,TS + change 16/16 Thecc1EG016792t1 552 19 3 TCt TCC S=S s4b212210 CR,PO,TS + silent 19/19 Thecc1EG016792t1 332 5 2 CcT CTT P>L s4b212430 CR,PO,TS + change 5/5 Thecc1EG016792t1 285 3 3 GGa GGC G=G s4b212477 CR,PO,TS,UF + silent 3/3 Thecc1EG016792t1 172 8 1 gGC AGC G>S s4b212590 PO,TS + change 8/13 Thecc1EG016792t1 172 5 1 GGC GGC G=G s4b212590 po,ts UF reads snp4o3uf.snp2cds.sum GeneID__________ bCDS Nrd Cdn Gcdn Tcdn dAA SNPid SNPgrp Thecc1EG016792t1 1302 55 3 ACG ACG T=T s4b207430 cr,po,ts Thecc1EG016792t1 1150 36 1 TGG TGG W=W s4b210547 CC Thecc1EG016792t1 1147 23 1 ATG ATG M=M s4b210550 cr,po,ts,uf Thecc1EG016792t1 1147 13 1 aTG CTG M>L s4b210550 CR,PO,TS,UF + change 13/36 Thecc1EG016792t1 1076 23 2 ACA ACA T=T s4b210621 cr Thecc1EG016792t1 1011 7 3 GAT GAT D=D s4b210686 po,ts Thecc1EG016792t1 825 11 3 AGC AGC S=S s4b211937 cc Thecc1EG016792t1 569 21 2 GGA GGA G=G s4b212193 cr,po,ts Thecc1EG016792t1 552 27 3 TCT TCT S=S s4b212210 cr,po,ts Thecc1EG016792t1 332 6 2 CCT CCT P=P s4b212430 cr,po,ts Thecc1EG016792t1 285 2 3 GGA GGA G=G s4b212477 cr,po,ts,uf Thecc1EG016792t1 172 5 1 GGC GGC G=G s4b212590 po,ts TC reads snp4o3tc.snp2cds.sum GeneID__________ bCDS Nrd Cdn Gcdn Tcdn dAA SNPid SNPgrp Thecc1EG016792t1 1302 97 3 ACG ACG T=T s4b207430 cr,po,ts Thecc1EG016792t1 1302 27 3 ACg ACA T=T s4b207430 CR,PO,TS + silent 27/124 reads Thecc1EG016792t1 1150 33 1 TGG TGG W=W s4b210547 CC Thecc1EG016792t1 1150 19 1 tGG CGG W>R s4b210547 cc + change 33/52 Thecc1EG016792t1 1147 28 1 aTG CTG M>L s4b210550 CR,PO,TS,UF + change 28/51 Thecc1EG016792t1 1147 23 1 ATG ATG M=M s4b210550 cr,po,ts,uf Thecc1EG016792t1 1076 12 2 ACA ACA T=T s4b210621 cr Thecc1EG016792t1 1011 4 3 GAT GAT D=D s4b210686 po,ts Thecc1EG016792t1 1011 3 3 GAt GAG D>E s4b210686 PO,TS + change 3/7 Thecc1EG016792t1 825 26 3 AGC AGC S=S s4b211937 cc Thecc1EG016792t1 569 9 2 GGA GGA G=G s4b212193 cr,po,ts Thecc1EG016792t1 552 11 3 TCT TCT S=S s4b212210 cr,po,ts Thecc1EG016792t1 332 10 2 CCT CCT P=P s4b212430 cr,po,ts Thecc1EG016792t1 285 4 3 GGA GGA G=G s4b212477 cr,po,ts,uf