Resource
| Id | Histone_ChIP-seq/ENCSR679OVD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR679OVD [biosample_summary="Homo sapiens esophagus tissue male adult (34 years)" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN870OPP|/analyses/ENCAN870OPP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF718TIL|/files/ENCFF718TIL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17668261 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-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 {ENCFF718TIL|/files/ENCFF718TIL/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF718TIL|/files/ENCFF718TIL/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.55. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR679OVD | float |
Histone_ChIP-seq_ENCSR679OVD |
Histone_ChIP-seq ENCSR679OVD [biosample_summary="Homo sapiens esophagus tissue male adult (34 years)" and target="H3K27ac"]
|
 |
[1.92, 66.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 55243257 | 1.72% | 76935 |
| chr1 | 6016357 | 2.42% | 7945 |
| chr2 | 4128023 | 1.70% | 6036 |
| chr3 | 3261269 | 1.64% | 4819 |
| chr4 | 1815209 | 0.95% | 2784 |
| chr5 | 2386580 | 1.31% | 3400 |
| chr6 | 2936388 | 1.72% | 4282 |
| chr7 | 2187588 | 1.37% | 3225 |
| chr8 | 1971134 | 1.36% | 3012 |
| chr9 | 2556563 | 1.85% | 3524 |
| chr10 | 2720090 | 2.03% | 3866 |
| chr11 | 3147546 | 2.33% | 4067 |
| chr12 | 2732742 | 2.05% | 3712 |
| chr13 | 1053594 | 0.92% | 1651 |
| chr14 | 2046298 | 1.91% | 2728 |
| chr15 | 1890041 | 1.85% | 2719 |
| chr16 | 2178610 | 2.41% | 2987 |
| chr17 | 3402628 | 4.09% | 4275 |
| chr18 | 946460 | 1.18% | 1465 |
| chr19 | 2865617 | 4.89% | 3487 |
| chr20 | 1654097 | 2.57% | 2346 |
| chr21 | 723644 | 1.55% | 1047 |
| chr22 | 1477830 | 2.91% | 1928 |
| chrX | 1108750 | 0.71% | 1580 |
| chrY | 36199 | 0.06% | 50 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 76935 | 145 | 20377 | 718.05 | 480 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF910HGC.bed.gz | 1.76 MB | 72a29b6d4ec01470154e6cfb09d4afb8 |
| ENCFF910HGC.tabix.bed.gz | 809.87 KB | 5002509d6d257c5815d463340f685b73 |
| ENCFF910HGC.tabix.bed.gz.tbi | 227.86 KB | c39fb166543e458db9a9fdc749634fda |
| genomic_resource.yaml | 3.22 KB | 75d1a86d299dc1e97d8ec5364493a0e5 |
| statistics/ |