The image below shows a screen shot of part of the file. Of particular interest here is the hg38#2914361 position that shows a mutation from G > T.
The next image shows the corresponding BAM file. This is about 640Mb.
The BAM file
Detail of BAM file location Detail of BAMOn row 253 hg38 #2914352 begins with a C then continues AAACCCAATTATAAAGAAGAAA. The bold T is the mutation at hg38#2914361 fron G > T. However, note on the row above at the same position it is a G. A closer look below:
Notice in row 523,(above the arrow), the 4 positions from location 2914361 is TTAT and the 2 rows above are GTAG. The same loctions in ybrowse.org are GTAT. The vcf file at 2914361 has T allele. Also interestingly only row 523 shows the mutation. position 2914363 is A but the vcf has no result. We can also see comparing row 523 with its mutation G > T at ~361 and T > G at ~364 compared with with rows 522 and 521 where the alleles are ancestral. Hence I don't usually use the VCF file.
My BAM file
The dowloaded BAM file is large at 657Mb. However it is easy to mapipulate once a BAM reader is installed. I use BAMSeek.jar from Google Code Archive as it does the job admirably. It is easy to use plus it has a fast scroll through the BAM file. It may be downloaded here: BAMseek download It is a .jar file and needs Java Runtime Environment to be installed. This may be downloaded (free) from Java at https://www.java.com/en/download/ The Jar file needs to be associaed with Java - not easy. However there is a small utility that it makes it easy to open .jar files with a normal double click. It may be downloaded (also free) from https://bitstorm.org/jarx/ The first time BAMSeek is used opening may be slow - a few seconds. Once the BAM file is opened there are a number of columns that I do not use and like in a spreadsheet may be made minimum width. The only columns of interest are Position and the Read Sequence/ data, as above.
GoTo Software used