Resource
| Id | Histone_ChIP-seq/ENCSR901JIL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR901JIL [biosample_summary="Homo sapiens mucosa of rectum tissue female adult (50 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (50 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN662WRU|/analyses/ENCAN662WRU/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF539EVS|/files/ENCFF539EVS/} processed by ChIP-seq ENCODE3 hg19 pipeline has 20458606 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 redacted alignments file {ENCFF539EVS|/files/ENCFF539EVS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. 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 redacted alignments file {ENCFF539EVS|/files/ENCFF539EVS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.20. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR901JIL | float |
Histone_ChIP-seq_ENCSR901JIL |
Histone_ChIP-seq ENCSR901JIL [biosample_summary="Homo sapiens mucosa of rectum tissue female adult (50 years)" and target="H3K4me1"]
|
 |
[1.59, 21.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 48985823 | 1.52% | 84238 |
| chr1 | 5320154 | 2.14% | 8909 |
| chr2 | 3547551 | 1.46% | 6396 |
| chr3 | 2668203 | 1.35% | 4780 |
| chr4 | 1559799 | 0.82% | 2974 |
| chr5 | 2247365 | 1.24% | 3977 |
| chr6 | 2427231 | 1.42% | 4581 |
| chr7 | 2002315 | 1.26% | 3665 |
| chr8 | 1675303 | 1.15% | 3016 |
| chr9 | 2268267 | 1.64% | 3782 |
| chr10 | 2331204 | 1.74% | 4098 |
| chr11 | 3032109 | 2.24% | 4928 |
| chr12 | 2378455 | 1.78% | 4088 |
| chr13 | 855875 | 0.75% | 1619 |
| chr14 | 1868334 | 1.75% | 3114 |
| chr15 | 1869045 | 1.83% | 3167 |
| chr16 | 2186166 | 2.42% | 3570 |
| chr17 | 3398786 | 4.08% | 5266 |
| chr18 | 794705 | 0.99% | 1516 |
| chr19 | 2500803 | 4.27% | 3883 |
| chr20 | 1549333 | 2.40% | 2582 |
| chr21 | 618189 | 1.32% | 1086 |
| chr22 | 1461950 | 2.88% | 2286 |
| chrX | 424681 | 0.27% | 955 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84238 | 165 | 8115 | 581.52 | 464 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF938BVK.bed.gz | 1.56 MB | 480e1fcf8ecb09f7cde45b8d95854799 |
| ENCFF938BVK.tabix.bed.gz | 809.77 KB | 8f5896b4aa9110b6b752fd3ccbeb5c9b |
| ENCFF938BVK.tabix.bed.gz.tbi | 248.3 KB | 29daed2b2ae3620d9f7bd1d25dee514a |
| genomic_resource.yaml | 3.28 KB | 072e690155adb1ab2453e40ba2b3144b |
| statistics/ |