{{ details.seq_length }} bp
{{ "{:.2f}".format(details.gc_content) }}%
Locus: {{ details.marker_offsets }}
GRCh38 {{ details.chromosome }}: {{ details.chrom_offsets }}
In this table, "Mapped Reads" refers to the total number of reads that mapped to the marker reference sequence. "Mapped Rate" refers to the proportion of reads mapped compared to what we would expect to see with perfectly even coverage across all markers: that is, a "Mapped Rate" of > 1.0 indicates higher than expected coverage and < 1.0 indicates lower than expected coverage. "Repetitive Reads" and "Repetitive Rate" refer to the number and percentage of reads that map to the marker reference, but preferentially map elsewhere when aligned to the entire genome. N/A values in these columns indicate that the marker definition file does not have GRCh38 coordinates for all SNPs, which are required for repetitive read analysis.
Sample | Mapped Reads | Mapped Rate | Repetitive Reads | Repetitive Rate | ||
---|---|---|---|---|---|---|
{{sample}} | {{"{:,d}".format(sample_data.loc[details.identifier,'ReadCount'])}} | {{"{:.2f}".format(sample_data.loc[details.identifier, 'ExpectedObservedRatio'])}} | {% if isna(sample_data.loc[details.identifier, 'RepetitiveReads']) %}N/A | N/A | {% else %}{{"{:,d}".format(sample_data.loc[details.identifier, 'RepetitiveReads'])}} | {{"{:.2f}".format(sample_data.loc[details.identifier, 'RepetitiveRate']*100)}}% | {% endif %}
The number and percentage of reads which were successfully haplotyped in each sample. Reads that span all SNPs of interest in the marker are examined; all other reads are discarded.
Sample | Typed Reads | Total Reads | Typing Rate |
---|---|---|---|
{{sample}} | {{ stats.successful }} | {{ stats.total_reads }} | {{ stats.typing_rate }} |
The following plots show all MH alleles (haplotypes) observed at this marker, sample by sample. In each plot, the red dotted line shows the threshold used for that sample to discriminate between true MH alleles and noise/artifacts and make a final genotype determination.
{% for sample in typing_summary.keys(): %}