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Contents

Schemas

Contents

• Schemas

  • PoreCConcatemerRecord

  • PoreCContactRecord

  • PoreCRecord

  • FragmentRecord

  • AlignmentRecord

PoreCConcatemerRecord

PoreCConcatemerRecord

type	object
properties
read_name	Read Name
	The original read name
	type	string
	minLength	1
read_length	Read Length
	The length of the read in bases
	type	integer
	minimum	1
read_idx	Read Idx
	Unique integer ID of the read
	type	integer
	minimum	0
read_order	Read Order
	The number of monomers for this read
	type	integer
	minimum	0
num_fragments	Num Fragments
	The number of unique restriction fragments represented in the concatemer
	type	integer
	minimum	0
total_contacts	Total Contacts
	The total (direct + indirect) number of contacts for this read
	type	integer
	minimum	0
total_cis_contacts	Total Cis Contacts
	The total number of cis-contacts (direct + indirect) for this read
	type	integer
	minimum	0
total_trans_contacts	Total Trans Contacts
	The total number of trans-contacts (direct + indirect) for this read
	type	integer
	minimum	0
total_short_range_cis_contacts	Total Short Range Cis Contacts
	The total number of cis contacts < 20000 bases apart for this read
	type	integer
	minimum	0
total_long_range_cis_contacts	Total Long Range Cis Contacts
	The total number of cis contacts >= 20000 bases apart for this read
	type	integer
	minimum	0
direct_contacts	Direct Contacts
	The total number direct (adjacent on read) contacts for this read
	type	integer
	minimum	0
direct_cis_contacts	Direct Cis Contacts
	The number of direct cis-contacts for this read
	type	integer
	minimum	0
direct_trans_contacts	Direct Trans Contacts
	The number of direct trans-contacts for this read
	type	integer
	minimum	0
direct_short_range_cis_contacts	Direct Short Range Cis Contacts
	The number of direct cis contacts < 20000 bases apart for this read
	type	integer
	minimum	0
direct_long_range_cis_contacts	Direct Long Range Cis Contacts
	The number of direct cis contacts >= 20000 bases apart for this read
	type	integer
	minimum	0
indirect_contacts	Indirect Contacts
	The total number indirect (non-adjacent on read) contacts for this read
	type	integer
	minimum	0
indirect_cis_contacts	Indirect Cis Contacts
	The number of indirect cis-contacts for this read
	type	integer
	minimum	0
indirect_trans_contacts	Indirect Trans Contacts
	The number of indirect trans-contacts for this read
	type	integer
	minimum	0
indirect_short_range_cis_contacts	Indirect Short Range Cis Contacts
	The number of indirect cis contacts < 20000 bases apart for this read
	type	integer
	minimum	0
indirect_long_range_cis_contacts	Indirect Long Range Cis Contacts
	The number of indirect cis contacts >= 20000 bases apart for this read
	type	integer
	minimum	0
haplotype_phased_h_cis	Haplotype Phased H Cis
	The number of cis contacts where both members of the pair are phased, are part of the same phase group, and the haplotypes agree
	type	integer
	minimum	0
haplotype_phased_h_trans	Haplotype Phased H Trans
	The number of cis contacts where both members of the pair are phased, are part of the same phase group, but the haplotypes differ
	type	integer
	minimum	0
haplotype_phased_sets_differ	Haplotype Phased Sets Differ
	The number of cis contacts where both members of the pair are phased but the phase sets differ
	type	integer
	minimum	0
haplotype_semi_phased	Haplotype Semi Phased
	The number of cis contacts where one member of the pair is unphased
	type	integer
	minimum	0
haplotype_unphased	Haplotype Unphased
	The number of cis contacts where both members of the pair are unphased
	type	integer
	minimum	0
max_indirect_contact_genome_distance	Max Indirect Contact Genome Distance
	[‘The longest distance between alignment endpoints for all indirect contacts’]
	type	integer
	minimum	0
max_direct_contact_genome_distance	Max Direct Contact Genome Distance
	[‘The longest distance between alignment endpoints for all direct contacts’]
	type	integer
	minimum	0
max_indirect_contact_fragment_distance	Max Indirect Contact Fragment Distance
	[‘The longest distance between fragment midpoints for all indirect contacts’]
	type	integer
	minimum	0
max_direct_contact_fragment_distance	Max Direct Contact Fragment Distance
	[‘The longest distance between fragment midpoints for all direct contacts’]
	type	integer
	minimum	0

PoreCContactRecord

PoreCContactRecord

type	object
properties
read_name	Read Name
	The original read name
	type	string
	minLength	1
read_length	Read Length
	The length of the read in bases
	type	integer
	minimum	1
read_idx	Read Idx
	Unique integer ID of the read
	type	integer
	minimum	0
contact_is_direct	Contact Is Direct
	There are no intervening assigned restriction fragments on the read
	type	boolean
	default	False
contact_is_cis	Contact Is Cis
	Both alignments come from the same chromsome/contig
	type	boolean
	default	False
contact_read_distance	Contact Read Distance
	The distance between the end of the left alignment and the start of the right alignment on the read
	type	integer
	default	0
contact_genome_distance	Contact Genome Distance
	The distance between the end of the left alignment and the start of the right alignment (valid for cis contacts only)
	type	integer
	default	0
contact_fragment_adjacent	Contact Fragment Adjacent
	[‘A boolean to indicate if the contact is between the same or adjacent fragments’]
	type	boolean
	default	False
contact_fragment_distance	Contact Fragment Distance
	The distance between the midpoints of the assigned fragments (valid for cis contacts only)
	type	integer
	minimum	0
haplotype_pair_type	:ref:#/definitions/HaplotypePairType
align1_align_idx	Align1 Align Idx
	Unique integer ID of the first aligned segment
	type	integer
	minimum	0
align1_chrom	Align1 Chrom
	The chromosome/contig of the first aligned segment
	type	string
	minLength	1
align1_start	Align1 Start
	The zero-based start position on the genome of the alignment
	type	integer
	minimum	0
align1_end	Align1 End
	The end position on the genome of the alignment
	type	integer
	minimum	0
align1_strand	Align1 Strand
	The alignment strand
	type	boolean
align1_mapping_quality	Align1 Mapping Quality
	The mapping quality as calculated by the aligner
	type	integer
	maximum	255
	minimum	0
align1_align_score	Align1 Align Score
	The alignment score as calculated by the aligner
	type	integer
	minimum	0
align1_align_base_qscore	Align1 Align Base Qscore
	The mean read base score for the aligned segment (rounded to the nearest integer).
	type	integer
	minimum	0
align1_phase_set	Align1 Phase Set
	The ID of the phase set, often this is the start position of the phase block
	type	integer
	default	0
align1_phase_qual	Align1 Phase Qual
	The phred-scaled quality score of the haplotype assignment
	type	integer
	default	0
align1_haplotype	Align1 Haplotype
	The id of the haplotype within this block, usually set to 1 or 2. A value of -1 means that this alignment is unphased
	type	integer
	minimum	-1
	default	-1
align1_fragment_id	Align1 Fragment Id
	The UID of the restriction fragment assigned to this alignment
	type	integer
	minimum	0
	default	0
align1_fragment_start	Align1 Fragment Start
	The start point on the genome of this restriction fragment
	type	integer
	minimum	0
	default	0
align1_fragment_end	Align1 Fragment End
	The end point on the genome of this restriction fragment
	type	integer
	minimum	0
	default	0
align2_align_idx	Align2 Align Idx
	Unique integer ID of the first aligned segment
	type	integer
	minimum	0
align2_chrom	Align2 Chrom
	The chromosome/contig of the first aligned segment
	type	string
	minLength	1
align2_start	Align2 Start
	The zero-based start position on the genome of the alignment
	type	integer
	minimum	0
align2_end	Align2 End
	The end position on the genome of the alignment
	type	integer
	minimum	0
align2_strand	Align2 Strand
	The alignment strand
	type	boolean
align2_mapping_quality	Align2 Mapping Quality
	The mapping quality as calculated by the aligner
	type	integer
	maximum	255
	minimum	0
align2_align_score	Align2 Align Score
	The alignment score as calculated by the aligner
	type	integer
	minimum	0
align2_align_base_qscore	Align2 Align Base Qscore
	The mean read base score for the aligned segment (rounded to the nearest integer).
	type	integer
	minimum	0
align2_phase_set	Align2 Phase Set
	The ID of the phase set, often this is the start position of the phase block
	type	integer
	default	0
align2_haplotype	Align2 Haplotype
	The id of the haplotype within this block, usually set to 1 or 2. A value of -1 means that this alignment is unphased
	type	integer
	minimum	-1
	default	-1
align2_fragment_id	Align2 Fragment Id
	The UID of the restriction fragment assigned to this alignment
	type	integer
	minimum	0
	default	0
align2_fragment_start	Align2 Fragment Start
	The start point on the genome of this restriction fragment
	type	integer
	minimum	0
	default	0
align2_fragment_end	Align2 Fragment End
	The end point on the genome of this restriction fragment
	type	integer
	minimum	0
	default	0

PoreCRecord

PoreCRecord

An aligned segment from a BAM file with additional Pore-C related fields
type	object
properties
read_idx	Read Idx
	Unique integer ID of the read
	type	integer
	minimum	0
align_idx	Align Idx
	Unique integer ID of the aligned segment
	type	integer
	minimum	0
align_type	:ref:#/definitions/AlignmentType
chrom	Chrom
	The chromosome/contig the read is aligned to
	type	string
	minLength	1
start	Start
	The zero-based start position on the genome of the alignment
	type	integer
	minimum	0
end	End
	The end position on the genome of the alignment
	type	integer
	minimum	0
strand	Strand
	The alignment strand
	type	boolean
read_name	Read Name
	The original read name
	type	string
	minLength	1
read_length	Read Length
	The length of the read in bases
	type	integer
	minimum	1
read_start	Read Start
	The start coordinate on the read (0-based)
	type	integer
	minimum	0
read_end	Read End
	The end coordinate on the read (0-based)
	type	integer
	minimum	0
mapping_quality	Mapping Quality
	The mapping quality as calculated by the aligner
	type	integer
	maximum	255
	minimum	0
align_score	Align Score
	The alignment score as calculated by the aligner
	type	integer
	minimum	0
align_base_qscore	Align Base Qscore
	The mean read base score for the aligned segment (rounded to the nearest integer).
	type	integer
	minimum	0
phase_set	Phase Set
	The ID of the phase set, often this is the start position of the phase block
	type	integer
	default	0
phase_qual	Phase Qual
	The phred-scaled quality score of the haplotype assignment
	type	integer
	minimum	0
	default	0
haplotype	Haplotype
	The id of the haplotype within this block, usually set to 1 or 2. A value of -1 means that this alignment is unphased
	type	integer
	minimum	-1
	default	-1
pass_filter	Pass Filter
	Boolean flag, true if alignment passes all filters
	type	boolean
	default	True
filter_reason	:ref:#/definitions/AlignmentFilterReason
fragment_id	Fragment Id
	The UID of the restriction fragment assigned to this alignment
	type	integer
	minimum	0
	default	0
num_contained_fragments	Num Contained Fragments
	The number of restriction fragments completely contained within this alignment
	type	integer
	minimum	0
	default	0
num_overlapping_fragments	Num Overlapping Fragments
	The number of restriction fragments overlapping this alignment
	type	integer
	minimum	0
	default	0
overlap_length	Overlap Length
	The length of the overlap between alignment and fragment
	type	integer
	minimum	0
	default	0
fragment_start	Fragment Start
	The start point on the genome of this restriction fragment
	type	integer
	minimum	0
	default	0
fragment_end	Fragment End
	The end point on the genome of this restriction fragment
	type	integer
	minimum	0
	default	0
perc_of_alignment	Perc Of Alignment
	The percentage of the aligned segment that overlaps the assigned fragment
	type	number
	maximum	100
	minimum	0
	default	0.0
perc_of_fragment	Perc Of Fragment
	The percentage of the assigned restriction fragment that overlaps the aligned segment
	type	number
	maximum	100
	minimum	0
	default	0.0
is_contained	Is Contained
	Boolean flag to inidicate if the alignment is fully contained with the fragment
	type	boolean
	default	False

FragmentRecord

FragmentRecord

Meta-data associated with a restriction fragment
type	object
properties
chrom	Chrom
	The chromosome/contig the fragment is derived from
	type	string
	minLength	1
start	Start
	The zero-based start position on the genome of the fragment
	type	integer
	minimum	0
end	End
	The zero-based end position on the genome of the fragment
	type	integer
	minimum	0
fragment_id	Fragment Id
	Unique integer ID of the fragment, starts at 1
	type	integer
	minimum	1
fragment_length	Fragment Length
	Length of the fragment
	type	integer
	minimum	1

AlignmentRecord

AlignmentRecord

An alignment derived from a BAM file
type	object
properties
read_idx	Read Idx
	Unique integer ID of the read
	type	integer
	minimum	0
align_idx	Align Idx
	Unique integer ID of the aligned segment
	type	integer
	minimum	0
align_type	:ref:#/definitions/AlignmentType
chrom	Chrom
	The chromosome/contig the read is aligned to
	type	string
	minLength	1
start	Start
	The zero-based start position on the genome of the alignment
	type	integer
	minimum	0
end	End
	The end position on the genome of the alignment
	type	integer
	minimum	0
strand	Strand
	The alignment strand
	type	boolean
read_name	Read Name
	The original read name
	type	string
	minLength	1
read_length	Read Length
	The length of the read in bases
	type	integer
	minimum	1
read_start	Read Start
	The start coordinate on the read (0-based)
	type	integer
	minimum	0
read_end	Read End
	The end coordinate on the read (0-based)
	type	integer
	minimum	0
mapping_quality	Mapping Quality
	The mapping quality as calculated by the aligner
	type	integer
	maximum	255
	minimum	0
align_score	Align Score
	The alignment score as calculated by the aligner
	type	integer
	minimum	0
align_base_qscore	Align Base Qscore
	The mean read base score for the aligned segment (rounded to the nearest integer).
	type	integer
	minimum	0
phase_set	Phase Set
	The ID of the phase set, often this is the start position of the phase block
	type	integer
	default	0
phase_qual	Phase Qual
	The phred-scaled quality score of the haplotype assignment
	type	integer
	minimum	0
	default	0
haplotype	Haplotype
	The id of the haplotype within this block, usually set to 1 or 2. A value of -1 means that this alignment is unphased
	type	integer
	minimum	-1
	default	-1

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