Dear all,
I used sanger sequencing to confirm some SNPs that I "discovered" with a GAII experiment using samtools v0.1.7. For a "bunch" of reasons, I generated a new pileup file using v0.1.8. The pileup looks like this for v0.1.7:
scaffold_7 13782966 A R 155 155 49 354 G$G$G$G$G$.$g$g$g$G,,.g,...G...GGG.,,.G,,,GG,g,g....G..G.,G..Ggggggg.Gg,ggg.GGG.G.,gg...g,.Ggg.,gG.,,,gG....g..GGGG.,,..ggg.G.GGg,.G.GG.gGGG..GGG,.,g,...GG,g
.G,g..,ggG.G...g.,,,.gggG.,,,.GGgg,,,GGG....G,GGG.GG,.G.GG.,..G...ggG,.GG..gg..Gg,,GG.G..GG....G.,.,GgGGG.G.Gg,G.G,,,,,.GGG.G.G.G,GGG.GGggg,g,.GGG.GG,G,,,gg.G...g.,ggG....G,gg,.g,,GG.GG.G.g,^].^]G^]G^]G^]G^]G^].^F.^].^F.^F.^]g^].^],^]G^F
, .-....787-77.87-.........-78..787..7777----...--7....777787..78877......-777...87-.77-78-.7877...-.7.......773377733332873222337778778878777777777*7777777787787777777777777777877878787%7778777727778773777777277777733837737833877-..
7777777777-787.8.7-7778878..777.....7777888777.788777..-...8777878.7..-..77777.7..-777887.-..7...77778877-.88778888877-7.7. FF]]]FF]FFFFF]]FF]]]]]]FFFF]FF]]]]]FFFFFF]FFF]]FFF]]]FFF]]F]F]]]]FFFF]]FFFFFF]]]F]FFFF]]F]F]FFFFFFF]FFF]]FF]
]F]F]]]]]]F]F]]]]FF]F]]FF]]F]]]]FFFF]]]]]]F]FFF]FF]]]FF]FF]]F]]FF]]]FF]]]]]FFFFF]]]]FFF]]]FFFFFFFF]]FFFFFFF]]]]F]]]]]]]FF]FFFFFF]]]FFF]]F]]]]FFFF]]]]F]]FF]]F:FFFFF]]]]FFFF]]]]FFFF]FF]]]F]]]FFFFFFF]FFFF]]]]]FFF]]FF]]F]F]FFFFF]]FFF]]]]]]]]
And like this for v.0.1.8:
scaffold_7 13782966 A A 1 0 49 354 G$G$G$G$G$.$g$g$g$G,,.g,...G...GGG.,,.G,,,GG,g,g....G..G.,G..Ggggggg.Gg,ggg.GGG.G.,gg...g,.Ggg.,gG.,,,gG....g..GGGG.,,..ggg.G.GGg,.G.GG.gGGG..GGG,.,g,...GG,g
.G,g..,ggG.G...g.,,,.gggG.,,,.GGgg,,,GGG....G,GGG.GG,.G.GG.,..G...ggG,.GG..gg..Gg,,GG.G..GG....G.,.,GgGGG.G.Gg,G.G,,,,,.GGG.G.G.G,GGG.GGggg,g,.GGG.GG,G,,,gg.G...g.,ggG....G,gg,.g,,GG.GG.G.g,^].^]G^]G^]G^]G^]G^].^F.^].^F.^F.^]g^].^],^]G^F
, .-....787-77.87-.........-78..787..7777----...--7....777787..78877......-777...87-.77-78-.7877...-.7.......773377733332873222337778778878777777777*7777777787787777777777777777877878787%7778777727778773777777277777733837737833877-..
7777777777-787.8.7-7778878..777.....7777888777.788777..-...8777878.7..-..77777.7..-777887.-..7...77778877-.88778888877-7.7. FF]]]FF]FFFFF]]FF]]]]]]FFFF]FF]]]]]FFFFFF]FFF]]FFF]]]FFF]]F]F]]]]FFFF]]FFFFFF]]]F]FFFF]]F]F]FFFFFFF]FFF]]FF]
]F]F]]]]]]F]F]]]]FF]F]]FF]]F]]]]FFFF]]]]]]F]FFF]FF]]]FF]FF]]F]]FF]]]FF]]]]]FFFFF]]]]FFF]]]FFFFFFFF]]FFFFFFF]]]]F]]]]]]]FF]FFFFFF]]]FFF]]F]]]]FFFF]]]]F]]FF]]F:FFFFF]]]]FFFF]]]]FFFF]FF]]]F]]]FFFFFFF]FFFF]]]]]FFF]]FF]]F]F]FFFFF]]FFF]]]]]]]]
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How can the consensus quality and SNP quality go from 155 to 0 and 1?
Thanks
I used sanger sequencing to confirm some SNPs that I "discovered" with a GAII experiment using samtools v0.1.7. For a "bunch" of reasons, I generated a new pileup file using v0.1.8. The pileup looks like this for v0.1.7:
scaffold_7 13782966 A R 155 155 49 354 G$G$G$G$G$.$g$g$g$G,,.g,...G...GGG.,,.G,,,GG,g,g....G..G.,G..Ggggggg.Gg,ggg.GGG.G.,gg...g,.Ggg.,gG.,,,gG....g..GGGG.,,..ggg.G.GGg,.G.GG.gGGG..GGG,.,g,...GG,g
.G,g..,ggG.G...g.,,,.gggG.,,,.GGgg,,,GGG....G,GGG.GG,.G.GG.,..G...ggG,.GG..gg..Gg,,GG.G..GG....G.,.,GgGGG.G.Gg,G.G,,,,,.GGG.G.G.G,GGG.GGggg,g,.GGG.GG,G,,,gg.G...g.,ggG....G,gg,.g,,GG.GG.G.g,^].^]G^]G^]G^]G^]G^].^F.^].^F.^F.^]g^].^],^]G^F
, .-....787-77.87-.........-78..787..7777----...--7....777787..78877......-777...87-.77-78-.7877...-.7.......773377733332873222337778778878777777777*7777777787787777777777777777877878787%7778777727778773777777277777733837737833877-..
7777777777-787.8.7-7778878..777.....7777888777.788777..-...8777878.7..-..77777.7..-777887.-..7...77778877-.88778888877-7.7. FF]]]FF]FFFFF]]FF]]]]]]FFFF]FF]]]]]FFFFFF]FFF]]FFF]]]FFF]]F]F]]]]FFFF]]FFFFFF]]]F]FFFF]]F]F]FFFFFFF]FFF]]FF]
]F]F]]]]]]F]F]]]]FF]F]]FF]]F]]]]FFFF]]]]]]F]FFF]FF]]]FF]FF]]F]]FF]]]FF]]]]]FFFFF]]]]FFF]]]FFFFFFFF]]FFFFFFF]]]]F]]]]]]]FF]FFFFFF]]]FFF]]F]]]]FFFF]]]]F]]FF]]F:FFFFF]]]]FFFF]]]]FFFF]FF]]]F]]]FFFFFFF]FFFF]]]]]FFF]]FF]]F]F]FFFFF]]FFF]]]]]]]]
And like this for v.0.1.8:
scaffold_7 13782966 A A 1 0 49 354 G$G$G$G$G$.$g$g$g$G,,.g,...G...GGG.,,.G,,,GG,g,g....G..G.,G..Ggggggg.Gg,ggg.GGG.G.,gg...g,.Ggg.,gG.,,,gG....g..GGGG.,,..ggg.G.GGg,.G.GG.gGGG..GGG,.,g,...GG,g
.G,g..,ggG.G...g.,,,.gggG.,,,.GGgg,,,GGG....G,GGG.GG,.G.GG.,..G...ggG,.GG..gg..Gg,,GG.G..GG....G.,.,GgGGG.G.Gg,G.G,,,,,.GGG.G.G.G,GGG.GGggg,g,.GGG.GG,G,,,gg.G...g.,ggG....G,gg,.g,,GG.GG.G.g,^].^]G^]G^]G^]G^]G^].^F.^].^F.^F.^]g^].^],^]G^F
, .-....787-77.87-.........-78..787..7777----...--7....777787..78877......-777...87-.77-78-.7877...-.7.......773377733332873222337778778878777777777*7777777787787777777777777777877878787%7778777727778773777777277777733837737833877-..
7777777777-787.8.7-7778878..777.....7777888777.788777..-...8777878.7..-..77777.7..-777887.-..7...77778877-.88778888877-7.7. FF]]]FF]FFFFF]]FF]]]]]]FFFF]FF]]]]]FFFFFF]FFF]]FFF]]]FFF]]F]F]]]]FFFF]]FFFFFF]]]F]FFFF]]F]F]FFFFFFF]FFF]]FF]
]F]F]]]]]]F]F]]]]FF]F]]FF]]F]]]]FFFF]]]]]]F]FFF]FF]]]FF]FF]]F]]FF]]]FF]]]]]FFFFF]]]]FFF]]]FFFFFFFF]]FFFFFFF]]]]F]]]]]]]FF]FFFFFF]]]FFF]]F]]]]FFFF]]]]F]]FF]]F:FFFFF]]]]FFFF]]]]FFFF]FF]]]F]]]FFFFFFF]FFFF]]]]]FFF]]FF]]F]F]FFFFF]]FFF]]]]]]]]
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How can the consensus quality and SNP quality go from 155 to 0 and 1?
Thanks
