Thermo Scientific Ion Torrent A45727, Руководство пользователя

Страница: 149 / 163

File Description
Amplicon
coverage
summary
Coverage summary data used to create the Amplicon Coverage Chart. This file contains these
fields:
•
contig_id
: the name of the chromosome or contig of the reference for this amplicon.
•
contig_srt
: the start location of the amplicon target region.
This coordinate is 1-based, unlike the corresponding 0-based coordinate in the original
targets BED file.
•
contig_end
: the last base coordinate of this amplicon target region.
Note: The length of the amplicon target is given as tlen = (contig_end - cont 1).
•
region_id
: the ID for this amplicon as given as the 4th column of the targets BED file.
•
gene_id
: the gene symbol as given as the last field of the targets BED file.
•
gc_count
: the number of G and C bases in the target region. %GC = 100% * gc / tlen.
•
overlaps
: the number of times this target was overlapped by any read by at least one
base.
Individual reads might overlap multiple amplicons where the amplicon regions themselves
overlap.
•
fwd_e2e
: the number of assigned forward strand reads that read from one end of the
amplicon region to the other end.
•
rev_e2e
: the number of assigned reverse strand reads that read from one end of the
amplicon region to the other end.
•
total_reads
: the total number of reads assigned to this amplicon. This value is the sum
of
fwd_reads
and
rev_reads
and is the field that rows of this file are ordered by (then by
contig id
,
srt
and
end
).
•
fwd_reads
: the number of forward strand reads assigned to this amplicon.
•
rev_reads
: the number of reverse strand reads assigned to this amplicon.
•
cov20x
: the number of bases of the amplicon target that had at least 20 reads.
•
cov100x
: the number of bases of the amplicon target that had at least 100 reads.
•
cov500x
: the number of bases of the amplicon target that had at least 500 reads.
Chromosome
base coverage
summary
Base reads per chromosome summary data used to create the default view of the Reference
Coverage Chart. This file contains these fields:
•
chrom
: the name of the chromosome or contig of the reference.
•
start
: the coordinate of the first base in this chromosome. This is always 1.
•
end
: the coordinate of the last base of this chromosome. Also its length in bases.
•
fwd_reads
: the total number of forward strand base reads for the chromosome.
•
rev_reads
: the total number reverse strand base reads for the chromosome.
•
fwd_ontrg
(if present): the total number of forward strand base reads that were in at least
one target region.
•
seq_reads
: the total sequencing (whole) reads that are mapped to individual contigs.
Aligned reads
BAM file
Contains all aligned reads that are used to generate this report, in BAM format. This is the same
file that can be downloaded from the main report (for the specific barcode). See the current SAM
tools documentation for more file format information.
Aligned reads BAI
file
Binary BAM index file as required by some analysis tools and alignment viewers such as IGV. This
is the same file that can be downloaded from the main report (for the specific barcode).
Appendix D coverageAnalysis plugin in Genexus
™
Software
Output files generated by the coverageAnalysis plugin
D
Genexus
™
Integrated Sequencer User Guide 149