I have got PacBio data from a Sequel machine at a coverage > 50X. I have run it in SMRT Link with their Base Modification Detection algorithm. I am now trying to figure out how to interpret the output and where to find the information about the modified bases. One of the outputs is a GFF3 file. The top of this file looks like this:
> ##gff-version 3
...
> I kinModCall modified_base 1168 1168 31 - . coverage=48;context=TTAAACTAATTTCCAAAAATTTTGAACAGTTTTTAATACAA;IPDRatio=2.96
> I kinModCall modified_base 1497 1497 32 - . coverage=50;context=CTTGAAAACACGAATATCTGTTTAGACAATAGTTTTGCCAA;IPDRatio=3.19
> I kinModCall modified_base 1509 1509 33 - . coverage=48;context=CATGAAAAATTTCTTGAAAACACGAATATCTGTTTAGACAA;IPDRatio=2.84
> I kinModCall modified_base 1529 1529 39 - . coverage=46;context=AAGAAAAGACCAAGAAAAACCATGAAAAATTTCTTGAAAAC;IPDRatio=3.84
> I kinModCall modified_base 1904 1904 36 - . coverage=54;context=TAAAACCTGACAGAAAGAATTGGTCCCGTCATCTACTTTCT;IPDRatio=2.86
> I kinModCall modified_base 2152 2152 31 - . coverage=59;context=TTAAAAATTAATATAAAATCAGGGAAATTTTTTTAAATTTT;IPDRatio=2.98
> I kinModCall modified_base 2226 2226 36 - . coverage=63;context=TGGGCGGGGCGTCTCTGCCGGGAAAATTTTGCGTTTAAAAA;IPDRatio=2.59
> I kinModCall modified_base 2228 2228 34 - . coverage=52;context=CGTGGGCGGGGCGTCTCTGCCGGGAAAATTTTGCGTTTAAA;IPDRatio=2.98
> I kinModCall modified_base 2237 2237 33 - . coverage=60;context=GCACGGTTTCGTGGGCGGGGCGTCTCTGCCGGGAAAATTTT;IPDRatio=3.07
> I kinModCall modified_base 2240 2240 44 - . coverage=63;context=GCGGCACGGTTTCGTGGGCGGGGCGTCTCTGCCGGGAAAAT;IPDRatio=2.89
> I kinModCall modified_base 2311 2311 31 - . coverage=63;context=AAAATCGACGAAAATCGGTATAAAATCAAATAAAAATAGAA;IPDRatio=4.35
> I kinModCall modified_base 2313 2313 39 - . coverage=62;context=GAAAAATCGACGAAAATCGGTATAAAATCAAATAAAAATAG;IPDRatio=4.00
> I kinModCall modified_base 2314 2314 34 - . coverage=63;context=AGAAAAATCGACGAAAATCGGTATAAAATCAAATAAAAATA;IPDRatio=2.63
> I kinModCall modified_base 2333 2333 35 - . coverage=62;context=AAAAAAAAGAGAAAAAATGAGAAAAATCGACGAAAATCGGT;IPDRatio=3.77
> I kinModCall modified_base 2334 2334 35 - . coverage=63;context=CAAAAAAAAGAGAAAAAATGAGAAAAATCGACGAAAATCGG;IPDRatio=2.77
I expected something along the lines of 'chromosome I position 1497 methylcytosine', etc.
So it seems that the algorithm has detected modified bases at the following positions but it cannot call them, maybe because of a lack of coverage?
Update: the screenshot below shows there is no CSV file in the Data tab of the completed analysis.