NCBI
dbSNP

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Method Detail
Submitter Method Handle: KWOK
Submitter Method ID: OverlapSnpDetectionWithPolyBayes
Submitted method description:
GENERAL
These SNPs were discovered by automated computer analysis of overlapping regions of
large-insert human genomic clone sequences.
DATA PROCESSING
Data acquisition: Clone sequences were obtained directly from large-scale
sequencing centers. This was necessary because base quality sequences were not
present/available through GenBank.
Raw data processing: Clone sequences and accompanying base quality information
were checked for consistency. Finished ('base perfect', error rate lower than
1 in 10,000 bp) sequences with no associated base quality sequences were assigned
a uniform base quality value of 40 (1 in 10,000 bp error rate). Draft sequences
without base quality values were rejected. Processed sequences were entered into
a local database. A version of each sequence with known human repeats masked were
also stored. Repeat masking was performed with the program 'MASKERAID'.
Overlap detection: Putative overlaps were detected with the program 'WUBLAST'.
Several filtering steps followed in order to eliminate false overlap detection
results, i.e. similarities between a pair of clone sequences that arise due to
sequence duplication as opposed to true overlap: Total length of overlap, overall
percent similarity, number of sequence differences between nucleotides with
high base quality value 'high-quality mismatches'. Results were also compared to
results of restriction fragment mapping of genomic clones at Washington University
Genome Sequencing Center, finisher's reports on overlaps, and results of the
sequence contig building effort at the NCBI.
SNP detection: Overlapping pairs of clone sequence were analyzed for candidate
SNP sites with the 'POLYBAYES' SNP detection software. Sequence differences between
the pair of sequences were scored for the probability of representing true
seqeunce variation as opposed to seqeuncing error. This process requires the
presence of base quality values for both seqeunces. High-scoring candidates
were extracted. The search was restricted to substitution-type single base pair
variations.
PARAMETERS:
Specific parameter values are found in the batch method exception fields
EXPLANATION OF PARSABLE COMMENT FIELDS IN SNP RECORDS
SequenceLocalName1:
Name of the first clone in pair as obtained from sequencing center.
SequenceAccession1:
GenBank accession number of first clone as could be determined (may
not always be accurate).
SequenceSource1:
Contributing sequencing center of first clone.
SequencePhase1:
First clone is finished (FI) or draft quality (5X) sequence.
SequenceContigName1:
Sequence contig of first clone in which first allele was found (local
use only).
SequenceContigPosition1:
Position of first allele in sequence contig of first clone (local use
only).
SequenceLocalName2:
Name of the second clone in pair as obtained from sequencing center.
SequenceAccession2:
GenBank accession number of second clone as could be determined (may
not always be accurate or available).
SequenceSource2:
Contributing sequencing center of second clone.
SequencePhase2:
Second clone is finished (FI) or draft quality (5X) sequence.
SequenceContigName2:
Sequence contig of second clone in which first allele was found (local
use only).
SequenceContigPosition2:
Position of second allele in sequence contig of first clone (local use
only).
PolyBayesConfidence:
Confidence score of candidate SNP as computed by the POLYBAYES software.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
KWOK Assay OVLP-1-99 75
KWOK Assay OVLP-1-98 75
KWOK Assay OVLP-1-97 75
KWOK Assay OVLP-1-96 75
KWOK Assay OVLP-1-95 75
KWOK Assay OVLP-1-94 75
KWOK Assay OVLP-1-93 75
KWOK Assay OVLP-1-92 75
KWOK Assay OVLP-1-91 75
KWOK Assay OVLP-1-90 75
KWOK Assay OVLP-1-89 75
KWOK Assay OVLP-1-88 75
KWOK Assay OVLP-1-87 75
KWOK Assay OVLP-1-86 75
KWOK Assay OVLP-1-85 75
KWOK Assay OVLP-1-84 75
KWOK Assay OVLP-1-83 75
KWOK Assay OVLP-1-82 75
KWOK Assay OVLP-1-81 75
KWOK Assay OVLP-1-80 75
KWOK Assay OVLP-000621-2 78
KWOK Assay OVLP-000621-4 78
KWOK Assay OVLP-000621-5 78
KWOK Assay OVLP-000621-6 78
KWOK Assay OVLP-000621-7 78
KWOK Assay OVLP-000621-8 78
KWOK Assay OVLP-000621-9 78
KWOK Assay OVLP-000621-10 78
KWOK Assay OVLP-000621-11 78
KWOK Assay OVLP-000621-12 78
KWOK Assay OVLP-000621-13 78
KWOK Assay OVLP-000621-14 78
KWOK Assay OVLP-000621-15 78
KWOK Assay OVLP-000621-16 78
KWOK Assay OVLP-000621-17 78
KWOK Assay OVLP-000621-18 78
KWOK Assay OVLP-000621-19 78
KWOK Assay OVLP-000621-20 78
KWOK Assay OVLP-000621-3 78
KWOK Assay OVLP-000621-1 78
KWOK Assay OVLP-000804-1 85
KWOK Assay OVLP-000804-2 85
KWOK Assay OVLP-000804-3 85
KWOK Assay OVLP-000804-4 85
KWOK Assay OVLP-000804-5 85
KWOK Assay OVLP-000804-6 85
KWOK Assay OVLP-000804-7 85
KWOK Assay OVLP-000804-8 85
KWOK Assay OVLP-000804-9 85
KWOK Assay OVLP-000804-10 85
KWOK Assay OVLP-000804-11 85
KWOK Assay OVLP-000804-12 85
KWOK Assay OVLP-000804-13 85
KWOK Assay OVLP-000804-14 85
KWOK Assay OVLP-000804-15 85
KWOK Assay OVLP-000804-16 85
KWOK Assay OVLP-000804-17 85
KWOK Assay OVLP-000804-18 85
KWOK Assay OVLP-000804-19 85
KWOK Assay OVLP-000804-20 85
KWOK Assay OVLP-000804-101 85
KWOK Assay OVLP-000804-102 85
KWOK Assay OVLP-000804-103 85
KWOK Assay OVLP-000804-104 85
KWOK Assay OVLP-000804-105 85
KWOK Assay OVLP-000804-106 85
KWOK Assay OVLP-000804-107 85
KWOK Assay OVLP-000804-108 85
KWOK Assay OVLP-000804-109 85
KWOK Assay OVLP-000804-110 85
KWOK Assay OVLP-000804-111 85
KWOK Assay OVLP-000804-112 85
KWOK Assay OVLP-000804-113 85
KWOK Assay OVLP-000804-114 85
KWOK Assay OVLP-000804-115 85
KWOK Assay OVLP-000804-116 85
KWOK Assay OVLP-000804-117 85
KWOK Assay OVLP-000804-118 85
KWOK Assay OVLP-000804-119 85
KWOK Assay OVLP-000804-120 85
KWOK Assay OVLP-000925-1-0 86
KWOK Assay OVLP-000925-1-1 86
KWOK Assay OVLP-000925-1-2 86
KWOK Assay OVLP-000925-1-3 86
KWOK Assay OVLP-000925-1-4 86
KWOK Assay OVLP-000925-1-5 86
KWOK Assay OVLP-000925-1-6 86
KWOK Assay OVLP-000925-1-7 86
KWOK Assay OVLP-000925-1-8 86
KWOK Assay OVLP-000925-1-9 86
KWOK Assay OVLP-000925-1-10 86
KWOK Assay OVLP-000925-1-11 86
KWOK Assay OVLP-000925-1-12 86
KWOK Assay OVLP-000925-1-13 86
KWOK Assay OVLP-000925-1-14 86
KWOK Assay OVLP-000925-1-15 86
KWOK Assay OVLP-000925-1-16 86
KWOK Assay OVLP-000925-1-17 86
KWOK Assay OVLP-000925-1-18 86
KWOK Assay OVLP-000925-1-19 86
KWOK Assay OVLP-000925-2-0 86
KWOK Assay OVLP-000925-2-1 86
KWOK Assay OVLP-000925-2-2 86
KWOK Assay OVLP-000925-2-3 86
KWOK Assay OVLP-000925-2-4 86
KWOK Assay OVLP-000925-2-5 86
KWOK Assay OVLP-000925-2-6 86
KWOK Assay OVLP-000925-2-7 86
KWOK Assay OVLP-000925-2-8 86
KWOK Assay OVLP-000925-2-9 86
KWOK Assay OVLP-000925-2-10 86
KWOK Assay OVLP-000925-2-11 86
KWOK Assay OVLP-000925-2-12 86
KWOK Assay OVLP-000925-2-13 86
KWOK Assay OVLP-000925-2-14 86
KWOK Assay OVLP-000925-2-15 86
KWOK Assay OVLP-000925-2-16 86
KWOK Assay OVLP-000925-2-17 86
KWOK Assay OVLP-000925-2-18 86
KWOK Assay OVLP-000925-2-19 86
KWOK Assay OVLP-000925-4-0 86
KWOK Assay OVLP-000925-4-1 86
KWOK Assay OVLP-000925-4-2 86
KWOK Assay OVLP-000925-4-3 86
KWOK Assay OVLP-000925-4-4 86
KWOK Assay OVLP-000925-4-5 86
KWOK Assay OVLP-000925-4-6 86
KWOK Assay OVLP-000925-4-7 86
KWOK Assay OVLP-000925-4-8 86
KWOK Assay OVLP-000925-4-9 86
KWOK Assay OVLP-000925-4-10 86
KWOK Assay OVLP-000925-4-11 86
KWOK Assay OVLP-000925-4-12 86
KWOK Assay OVLP-000925-4-13 86
KWOK Assay OVLP-000925-4-14 86
KWOK Assay OVLP-000925-4-15 86
KWOK Assay OVLP-000925-4-16 86
KWOK Assay OVLP-000925-4-17 86
KWOK Assay OVLP-000925-4-18 86
KWOK Assay OVLP-000925-4-19 86
KWOK Assay OVLP-000925-5-0 86
KWOK Assay OVLP-000925-5-1 86
KWOK Assay OVLP-000925-5-2 86
KWOK Assay OVLP-000925-5-3 86
KWOK Assay OVLP-000925-5-4 86
KWOK Assay OVLP-000925-5-5 86
KWOK Assay OVLP-000925-5-6 86
KWOK Assay OVLP-000925-5-7 86
KWOK Assay OVLP-000925-5-8 86
KWOK Assay OVLP-000925-5-9 86
KWOK Assay OVLP-000925-5-10 86
KWOK Assay OVLP-000925-5-11 86
KWOK Assay OVLP-000925-5-12 86
KWOK Assay OVLP-000925-5-13 86
KWOK Assay OVLP-000925-5-14 86
KWOK Assay OVLP-000925-5-15 86
KWOK Assay OVLP-000925-5-16 86
KWOK Assay OVLP-000925-5-17 86
KWOK Assay OVLP-000925-5-18 86
KWOK Assay OVLP-000925-5-19 86
KWOK Assay OVLP-000925-3-0 86
KWOK Assay OVLP-000925-3-1 86
KWOK Assay OVLP-000925-3-2 86
KWOK Assay OVLP-000925-3-3 86
KWOK Assay OVLP-000925-3-4 86
KWOK Assay OVLP-000925-3-5 86
KWOK Assay OVLP-000925-3-6 86
KWOK Assay OVLP-000925-3-7 86
KWOK Assay OVLP-000925-3-8 86
KWOK Assay OVLP-000925-3-9 86
KWOK Assay OVLP-000925-3-10 86
KWOK Assay OVLP-000925-3-11 86
KWOK Assay OVLP-000925-3-12 86
KWOK Assay OVLP-000925-3-13 86
KWOK Assay OVLP-000925-3-14 86
KWOK Assay OVLP-000925-3-15 86
KWOK Assay OVLP-000925-3-16 86
KWOK Assay OVLP-000925-3-17 86
KWOK Assay OVLP-000925-3-18 86
KWOK Assay OVLP-000925-3-19 86