Resource
| Id | Histone_ChIP-seq/ENCSR559IFS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR559IFS [biosample_summary="Homo sapiens NCI-H929" and target="H2AFZ"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN523WKX|/analyses/ENCAN523WKX/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF477WIN|/files/ENCFF477WIN/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 18993481 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H2AFZ-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 {ENCFF477WIN|/files/ENCFF477WIN/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 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 {ENCFF477WIN|/files/ENCFF477WIN/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.25. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR559IFS | float |
Histone_ChIP-seq_ENCSR559IFS |
Histone_ChIP-seq ENCSR559IFS [biosample_summary="Homo sapiens NCI-H929" and target="H2AFZ"]
|
 |
[1.54, 13.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 42553191 | 1.32% | 66669 |
| chr1 | 3903494 | 1.57% | 5806 |
| chr2 | 3472649 | 1.43% | 5502 |
| chr3 | 2941233 | 1.48% | 4682 |
| chr4 | 3085440 | 1.62% | 5237 |
| chr5 | 3752335 | 2.07% | 5764 |
| chr6 | 2657055 | 1.56% | 4182 |
| chr7 | 2023229 | 1.27% | 3287 |
| chr8 | 2882808 | 1.99% | 4453 |
| chr9 | 1505222 | 1.09% | 2427 |
| chr10 | 1578185 | 1.18% | 2492 |
| chr11 | 2322134 | 1.72% | 3528 |
| chr12 | 1791713 | 1.34% | 2805 |
| chr13 | 263300 | 0.23% | 473 |
| chr14 | 1319812 | 1.23% | 2045 |
| chr15 | 1294896 | 1.27% | 1907 |
| chr16 | 1081931 | 1.20% | 1700 |
| chr17 | 1359126 | 1.63% | 2046 |
| chr18 | 1386312 | 1.72% | 2191 |
| chr19 | 1242729 | 2.12% | 1837 |
| chr20 | 839099 | 1.30% | 1262 |
| chr21 | 521467 | 1.12% | 883 |
| chr22 | 509005 | 1.00% | 772 |
| chrX | 820017 | 0.53% | 1388 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 66669 | 195 | 3846 | 638.28 | 532 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF813NNK.bed.gz | 1.53 MB | e14ef9447d7a4469dedd8c6223f73e2c |
| ENCFF813NNK.tabix.bed.gz | 705.24 KB | 40e5796210e84758ba7fb6272c0b8f12 |
| ENCFF813NNK.tabix.bed.gz.tbi | 343.92 KB | 280da08a5c712da546e4377b63346bea |
| genomic_resource.yaml | 3.19 KB | 2c95418ca7f0d8890e44e9faaabc8f29 |
| statistics/ |