ITV-Corumba-062018 Files

In this folder, two files are stored per metagenomic sample, the first one corresponds to the forward reads (containing the text R1 along with the name of the sample within the filename) and the second corresponding to the reverse reads (containing the text R2 within the filename). All files are in HTML format and can be viewed in any current browser (such as Google Chrome and Mozilla Firefox) after download. Each report presents 12 sections, briefly described below. All statistics were obtained using the FastQC v0.11.5 tool, using standard parameters. A more comprehensive description of each section of this report, including possible errors and warnings, can be found in the tool documentation, available at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3% 20Analysis% 20Modules.

1) Basic Statistics

This section presents 7 simple information of the file which stores the reads of the analyzed (meta)genomic sample: 1) the filename, 2) the type of the file, 3) the type of encoding used to produce the file, 4) the numberof reads contained in the file, 5) the number of reads that did not pass the quality test (the filtering functionality of the tool was not used), 6) minimum and maximum reads lengths and 7) %GC along all reads (that is, the percentage of C or G found in the sequences).

2) Per base sequence quality

This section presents a box chart that briefly indicates the quality presented by the reads in each of their positions. In each box, the red line indicates the median; the yellow rectangles indicate the second and third quartiles; the upper and lower lines indicate the range of 10% to 90% of the points; and the blue line indicates the average quality.

3) Per tile sequence quality

This section shows a graph which indicates the average quality deviation of each of the tiles of the sequencer (name given to small areas of the image treated by the sequencer) at each position of the read, in a scale varying from blue to red. Thus, the colors closest to the blue indicate that the quality of the respective tile is equivalent to the quality of the others, while colors closer to the red indicate that the tile had worse quality than the others at the specific position. Ideally, this graphic has to be all colored in blue.

4) Per sequence quality scores

This section displays a graph that shows the distribution of reads along their respective average qualities.

5) Per base sequence content

This section shows a graph which shows the percentage of occurrence of each of the bases (A, C, T and G) along each of the positions of the reads.

6) Per sequence GC content

This section displays a graph that shows the distribution of reads along their respective %GC along with a modelled normal distribution of GC contents.

7) Per base N content

This section shows a graph which shows the percentage of occurrence of the letter N in the nucleotide sequences along each of the positions of the reads. The letter N is inserted by the sequencer when the base read could not be correctly identified with sufficient confidence.

8) Sequence Length Distribution

This section displays a graph that shows the distribution of reads along their respective sizes.

9) Sequence Duplication Levels

This section displays a graph that indicates the percentages of duplicate sequence considering different levels of duplication. The low level of duplication may indicate a high coverage rate of the complete genomic sequence, while the high level of duplication may indicate some type of enrichment (such as PCR amplification).

10) Overrepresented sequences

This section presents, if any, all over-represented sequences in the sample, which may indicate, among other hypotheses, that the library is contaminated.

11) Adapter Content

This section shows a graph that indicates the percentage of adapters found along reads positions. The presence of adapters does not correspond to a problem, but indicates that the sequences need to be trimmed to remove the adapters for the downstream analyzes.
 
12) Kmer Content

This section displays a graph indicating which are the six most frequent 7-mers (subsequences from reads with 7 nucleotides) among the reads, indicating the percentage of occurrence (log-scale) of each of them along the reads positions. Additional information on these and other 7-mers found is provided.