Dear Gviz Users,

i have a problem with Gviz package. I run this code:

C = "unitig_8_Part_Chr"
S = 524
E = 16706

txdb <-makeTxDbFromGFF("~/pathos/CQ2PacBio/sortedBams/coverage/overlap/CQ2Annot.gff3", format = "gff3")
ref = GeneRegionTrack(txdb, chromosome=C, start= S, end= E, name = "Reference", fill = "#40BAF7", rot.title = 0)
sTrack<-SequenceTrack("~/pathos/CQ2PacBio/VDAG_CQ2_11_01_2016.fasta")
chromosome(sTrack) <- C

BP2 = "~/pathos/CQ2PacBio/sortedBams/BP2.mod.bam.sorted.bam"
v4 = "~/pathos/CQ2PacBio/sortedBams/v4.bam.sorted.bam"
V117 = "~/pathos/CQ2PacBio/sortedBams/V117.bam.sorted.bam"
V991 = "~/pathos/CQ2PacBio/sortedBams/V991.mod.bam.sorted.bam"
T9 = "~/pathos/CQ2PacBio/sortedBams/T9.mod.bam.sorted.bam"
cotton15DPI = "~/pathos/CQ2PacBio/RNAseq/Cotton15DPIChinaAligned.sortedByCoord.out.bam"

bamBP2 <- AlignmentsTrack(BP2, isPaired = FALSE, name = "BP2",  rot.title = 0)
bamv4 <- AlignmentsTrack(v4, isPaired = FALSE, name = "v4",  rot.title = 0)
bamV117 <- AlignmentsTrack(V117, isPaired = FALSE, name = "V117", rot.title = 0)
bamV991 <- AlignmentsTrack(V991, isPaired = FALSE, name = "V991",  rot.title = 0)
bamT9 <- AlignmentsTrack(T9, isPaired = FALSE, name = "T9",  rot.title = 0)
bamcotton15DPI <- AlignmentsTrack(cotton15DPI, isPaired = FALSE, name = "cotton15DPI",  rot.title = 0)

plotTracks(c(ref, bamcotton15DPI,bamBP2,bamv4,bamV117,bamV991,bamT9,sTrack), chrom = C, from = S, to = E,  sizes = c(5,4,4,4,4,4,4,1))

plotTracks(c(ref, sTrack, bamT9), chrom = C, from = S, to = E,  sizes = c(5,1,4))

and I should have a pot where the first three bam file should show SNPs over the region while the bottom three should not show any SNPs. However, this is not the case. All the tracks display SNPs when plotted. Can anyone help, plsease?

Cheers

Luigi