No matter that I never looked at any of them, ever, and that they remained thrust deep in their manila folders in the depths of filing cabinets and yellowing boxes imprinted with the logos of appliances long since defunct — they were there and they gave me weight.
We identified 85 genes that were positively correlated with OsSMF1 in rice using the RAN under the tested conditions, with a minimum correlation value of 0.55 and a depth of 1 (Additional file 3: Table S2, Additional file 4: Figure S3).
We performed several experimental replicates for each kit, and sequenced the WGA product of each single cell a mean depth of ~0.5X (Additional file 1: Table S1 and Additional file 2: Table S2).
(Additional file 2: Table S2) More than 90% of the genome was covered by a minimum read depth of 20 (Additional file 2: Figure S1 and S2).
Sequencing was performed at The Institute for Molecular Medicine Finland (FIMM) using Illumina HiSeq 1500 with sequencing depth of 100×, and files were processed with their Variant Calling Pipeline.
Based on the next-generation sequencing data from 1765 rice varieties, a total of 7,100,998,643 publicly sequenced reads were downloaded from the NCBI National Center for Biotechnology Informationn) website, with an average length of 86.56 bp; the sequencing depth ranged from 0.03× (GP133) to 118.42× (Oryza-brachyantha), with an average depth of 1.89× (Additional file 1: Table S1).
On examining the remaining 97 mismatch heterozygous SNPs, the read depth in these regions ranges from 2 35 with a mean depth of 14 (Additional file 13: Table S9).
Of these, 65 had an average read depth of >100× (Additional file 1: Table S3), raising the possibility that they function as novel protein-coding sequences.
De novo assembly of the 5MgS reads resulted in 7,319 contigs with length ≥ 500 bp and average coverage depth of 20x (Additional file 1: Figure S1).
The exomes of tumor specimens in the discovery cohort were covered at a mean depth of 116× (Additional file 1: Table S2).
These genes were sequenced in a prevalence set of 60 treatment-naive snap-frozen OTSCC specimens by targeted sequencing with an average depth of 136× (Additional file 11).
