Resource
| Id | Histone_ChIP-seq/ENCSR510NXV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR510NXV [biosample_summary="Homo sapiens gastroesophageal sphincter tissue female adult (53 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (53 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN297RYO|/analyses/ENCAN297RYO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF113CGU|/files/ENCFF113CGU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19133165 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF113CGU|/files/ENCFF113CGU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF113CGU|/files/ENCFF113CGU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.07. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR510NXV | float |
Histone_ChIP-seq_ENCSR510NXV |
Histone_ChIP-seq ENCSR510NXV [biosample_summary="Homo sapiens gastroesophageal sphincter tissue female adult (53 years)" and target="H3K4me3"]
|
 |
[1.24, 78.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 52873628 | 1.64% | 36406 |
| chr1 | 5214235 | 2.09% | 3546 |
| chr1_KI270712v1_random | 2772 | 1.57% | 3 |
| chr1_KI270713v1_random | 1785 | 4.38% | 4 |
| chr1_KI270714v1_random | 409 | 0.98% | 1 |
| chr2 | 3659482 | 1.51% | 2538 |
| chr3 | 3037043 | 1.53% | 2059 |
| chr4 | 2195891 | 1.15% | 1513 |
| chr5 | 2488138 | 1.37% | 1702 |
| chr6 | 2939563 | 1.72% | 1996 |
| chr7 | 2594842 | 1.63% | 1810 |
| chr8 | 1983848 | 1.37% | 1441 |
| chr9 | 2311418 | 1.67% | 1581 |
| chr9_KI270717v1_random | 919 | 2.29% | 1 |
| chr10 | 2412184 | 1.80% | 1805 |
| chr11 | 2836109 | 2.10% | 1829 |
| chr12 | 2775814 | 2.08% | 1885 |
| chr13 | 1129632 | 0.99% | 834 |
| chr14 | 1682428 | 1.57% | 1124 |
| chr14_GL000009v2_random | 388 | 0.19% | 1 |
| chr15 | 1710077 | 1.68% | 1181 |
| chr16 | 2006859 | 2.22% | 1423 |
| chr17 | 2995052 | 3.60% | 1979 |
| chr17_GL000205v2_random | 2846 | 1.53% | 3 |
| chr18 | 909426 | 1.13% | 673 |
| chr19 | 3255846 | 5.55% | 2228 |
| chr20 | 1407690 | 2.18% | 973 |
| chr21 | 517243 | 1.11% | 390 |
| chr22 | 1232498 | 2.43% | 850 |
| chr22_KI270733v1_random | 659 | 0.37% | 2 |
| chrUn_GL000195v1 | 1284 | 0.70% | 3 |
| chrUn_GL000218v1 | 344 | 0.21% | 1 |
| chrUn_GL000219v1 | 4694 | 2.62% | 5 |
| chrUn_GL000220v1 | 720 | 0.44% | 1 |
| chrUn_KI270438v1 | 1335 | 1.19% | 3 |
| chrUn_KI270467v1 | 944 | 24.08% | 2 |
| chrX | 1559211 | 1.00% | 1016 |
| 3330 contigs with no values (184637393 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36406 | 210 | 24177 | 1452.33 | 1033 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF733UYO.bed.gz | 990.38 KB | 77f06c3919902793da7d29dbc5a4150c |
| ENCFF733UYO.tabix.bed.gz | 419.67 KB | 202625b8327962824b01389b22419d32 |
| ENCFF733UYO.tabix.bed.gz.tbi | 201.87 KB | c4df440b2d2486f9bc47999ebcab7d72 |
| genomic_resource.yaml | 3.29 KB | f11a471cad90c784b5948be32d5f624f |
| statistics/ |