QC description spreadsheets

HicQualityMetric

sequenced_reads

Number of total reads sequenced for library

sequenced_read_pairs

Number of total read pairs sequenced for library

no_chimera_found

Number of reads where no chimera was found

0_alignments

Number of reads that did not align to the reference genome

1_alignment

Number of reads that align to one position in the reference genome

1_alignment_unique

Number of unique reads that align to one position in the reference genome

1_alignment_duplicates

Number of duplicate reads that align to one position in the reference genome

2_alignments

Number of reads that align to two positions in the reference genome

2_alignments_a_b

Number of reads that align to two positions in the reference genome of the type A...B

2_alignment_duplicates

Number of duplicate reads that align to two positions in the reference genome

2_alignment_unique

Number of unique reads that align to two positions in the reference genome

2_alignments_a1_a2b_a1b2_b1a2

Number of reads that align to two positions in the reference genome of the type A1...A2B; A1B2...B1A2

3_or_more_alignments

Number of reads that align to three or more positions in the reference genome

pct_no_chimera_found

Percent of reads where no chimera was found

pct_0_alignments

Percent of reads that did not align to the reference genome

pct_1_alignment

Percent of reads that align to one position in the reference genome

pct_1_alignment_unique

Percent of unique reads that align to one position in the reference genome

pct_1_alignment_duplicates

Percent of duplicate reads that align to one position in the reference genome

pct_sequenced_1_alignment_unique

Percent of unique reads that align to one position in the reference genome

pct_sequenced_1_alignment_duplicates

Percent of duplicate reads that align to one position in the reference genome

pct_2_alignments

Percent of reads that align to two positions in the reference genome

pct_2_alignment_unique

Percent of unique reads that align to two positions in the reference genome

pct_2_alignment_duplicates

Percent of duplicate reads that align to two positions in the reference genome

pct_2_alignments_a_b

Percent of reads that align to two positions in the reference genome of the type A...B

pct_2_alignments_a1_a2b_a1b2_b1a2

Percent of reads that align to two positions in the reference genome of the type A1...A2B; A1B2...B1A2

pct_sequenced_2_alignment_unique

Percent of unique reads that align to two positions in the reference genome

pct_sequenced_2_alignment_duplicates

Percent of duplicate reads that align to two positions in the reference genome

pct_3_or_more_alignments

Percent of reads that align to three or more positions in the reference genome

pct_unique_total_duplicates

Percent of duplicate reads that align to the reference genome

pct_unique_total_unique

Percent of unique reads that align to the reference genome

one_or_both_reads_unmapped

Number of read pairs where one or both reads is unmapped

pct_one_or_both_reads_unmapped

Percent of read pairs where one or both reads is unmapped

ligation_motif_present

Number of reads containing a ligation motif

pct_ligation_motif_present

Percent of reads containing a ligation motif

avg_insert_size

Average insert size

total_unique

Number of unique reads that align to the reference genome

pct_sequenced_total_unique

Percent of unique reads that align to the reference genome

total_duplicates

Number of duplicate reads that align to the reference genome

pct_sequenced_total_duplicates

Percent of duplicate reads that align to the reference genome

library_complexity_estimate

Estimate of Library Complexity

library_complexity_estimate_1_alignment

Estimate of Library Complexity (for reads with one alignment)

library_complexity_estimate_2_alignments

Estimate of Library Complexity (for reads with two alignments)

library_complexity_estimate_1_and_2_alignments

Estimate of Library Complexity (for reads with one and two alignments)

intra_fragment_reads

Number of intra-fragment reads

pct_sequenced_intra_fragment_reads

Percent of intra-fragment reads

pct_unique_intra_fragment_reads

Percent of unique intra-fragment reads

below_mapq_threshold

Number of reads below the mapQ threshold

pct_sequenced_below_mapq_threshold

Percent of reads below the mapQ threshold

pct_unique_below_mapq_threshold

Percent of unique reads below the mapQ threshold

hic_contacts

Number of Hi-C contacts

pct_sequenced_hic_contacts

Percent of Hi-C contacts

pct_unique_hic_contacts

Percent of unique Hi-C contacts

pct_5_prime_bias_long_range

Percent of read ends from long range contacts mapping closer to the 5’ end of the fragment

pct_3_prime_bias_long_range

Percent of read ends from long range contacts mapping closer to the 3’ end of the fragment

lior_convergence

Distance in basepairs at which left, right, inner, and outer pair types converge

pct_left_pair_type

Percentage of Hi-C contacts with left pair type

pct_right_pair_type

Percentage of Hi-C contacts with right pair type

pct_inner_pair_type

Percentage of Hi-C contacts with inner pair type

pct_outer_pair_type

Percentage of Hi-C contacts with outer pair type

inter_chromosomal

Number of inter-chromosomal Hi-C contacts

pct_sequenced_inter_chromosomal

Percent of inter-chromosomal Hi-C contacts

pct_unique_inter_chromosomal

Percent of unique inter-chromosomal Hi-C contacts

intra_chromosomal

Number of intra-chromosomal Hi-C contacts

pct_sequenced_intra_chromosomal

Percent of intra-chromosomal Hi-C contacts

pct_unique_intra_chromosomal

Percent of unique intra-chromosomal Hi-C contacts

short_range_less_than_500bp

Number of intra-chromosomal Hi-C contacts with loci less than 500 basepairs apart

pct_sequenced_short_range_less_than_500bp

Percent of intra-chromosomal Hi-C contacts with loci less than 500 basepairs apart

pct_unique_short_range_less_than_500bp

Percent of unique intra-chromosomal Hi-C contacts with loci less than 500 basepairs apart

short_range_500bp_to_5kb

Number of intra-chromosomal Hi-C contacts with loci between 500 basepairs and 5 kilobases apart

pct_sequenced_short_range_500bp_to_5kb

Percent of intra-chromosomal Hi-C contacts with loci between 500 basepairs and 5 kilobases apart

pct_unique_short_range_500bp_to_5kb

Percent of unique intra-chromosomal Hi-C contacts with loci between 500 basepairs and 5 kilobases apart

short_range_5kb_to_20kb

Number of intra-chromosomal Hi-C contacts with loci between 5 and 20 kilobases apart

pct_sequenced_short_range_5kb_to_20kb

Percent of intra-chromosomal Hi-C contacts with loci between 5 and 20 kilobases apart

pct_unique_short_range_5kb_to_20kb

Percent of unique intra-chromosomal Hi-C contacts with loci between 5 and 20 kilobases apart

long_range_greater_than_20kb

Number of intra-chromosomal Hi-C contacts with loci greater than 20 kilobases apart

pct_sequenced_long_range_greater_than_20kb

Percent of intra-chromosomal Hi-C contacts with loci greater than 20 kilobases apart

pct_unique_long_range_greater_than_20kb

Percent of unique intra-chromosomal Hi-C contacts with loci greater than 20 kilobases apart