MicroHapulator Report: Marker Detail

Marker Length

{{marker_details_table.loc[markername,'Length']}} bp

%GC content

{{marker_details_table.loc[markername,'GC']}}%

SNP Offsets

Locus: {{marker_details_table.loc[markername,'Offsets']}}

{% if not isna(marker_details_table.loc[markername,"Chrom"]) %}

GRCh38 {{marker_details_table.loc[markername,"Chrom"]}}: {{marker_details_table.loc[markername,"Hg38Offset"]}}

{% endif %}

Marker Sequence (SNPs in red)

Read Mapping

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. "Off Target Reads" and "Off Target 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 off-target analysis.

{% for sample, sample_data in mapping_rates.items()%} {% if isna(sample_data.loc[markername, 'OffTargetReads']) %} {% else %} {% endif %} {% endfor %}

Sample	Mapped Reads	Mapped Rate	Off Target Reads	Off Target Rate
{{sample}}	{{"{:,d}".format(sample_data.loc[markername,'ReadCount'])}}	{{"{:.2f}".format(sample_data.loc[markername, 'ExpectedObservedRatio'])}}	N/A	N/A	{{"{:,d}".format(sample_data.loc[markername, 'OffTargetReads'])}}	{{"{:.2f}".format(sample_data.loc[markername, 'OffTargetRate']*100)}}%

Haplotype Calling

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.

{% for sample, sample_data in typing_rates.items()%} {% endfor %}

Sample	Typed Reads	Total Reads	Typing Rate
{{sample}}	{{ "{:,.0f}".format(sample_data.loc[markername, 'TypedReads']) }}	{{ "{:,.0f}".format(sample_data.loc[markername, 'TotalReads'])}}	{{ "{:.2f}".format(sample_data.loc[markername, 'TypingRate'] * 100)}}%

Genotype Calls

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_rates.keys(): %} {% endfor %}