Resource
| Id | Histone_ChIP-seq/ENCSR000AMH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AMH [biosample_summary="Homo sapiens H1" and target="H4K20me1"] |
| Description |
status: archived biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN708WXQ|/analyses/ENCAN708WXQ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF644BVX|/files/ENCFF644BVX/} processed by ChIP-seq ENCODE3 hg19 pipeline has 13486681 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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_not_compliant: Processed alignments file {ENCFF706GWV|/files/ENCFF706GWV/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11026534 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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 alignments file {ENCFF706GWV|/files/ENCFF706GWV/} 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 alignments file {ENCFF706GWV|/files/ENCFF706GWV/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.62. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AMH | float |
Histone_ChIP-seq_ENCSR000AMH |
Histone_ChIP-seq ENCSR000AMH [biosample_summary="Homo sapiens H1" and target="H4K20me1"]
|
 |
[2.05, 11.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 16696241 | 0.52% | 52168 |
| chr1 | 1551005 | 0.62% | 4972 |
| chr2 | 1226705 | 0.51% | 4010 |
| chr3 | 883495 | 0.45% | 2876 |
| chr4 | 638977 | 0.34% | 2042 |
| chr5 | 870481 | 0.48% | 2700 |
| chr6 | 932125 | 0.55% | 2689 |
| chr7 | 869176 | 0.55% | 2695 |
| chr8 | 759521 | 0.52% | 2265 |
| chr9 | 670716 | 0.48% | 2175 |
| chr10 | 767240 | 0.57% | 2344 |
| chr11 | 777908 | 0.58% | 2534 |
| chr12 | 780785 | 0.59% | 2551 |
| chr13 | 346266 | 0.30% | 1129 |
| chr14 | 471944 | 0.44% | 1520 |
| chr15 | 545419 | 0.53% | 1699 |
| chr16 | 848276 | 0.94% | 2555 |
| chr17 | 876632 | 1.05% | 2718 |
| chr18 | 207594 | 0.26% | 744 |
| chr19 | 1075159 | 1.83% | 3068 |
| chr20 | 584921 | 0.91% | 1732 |
| chr21 | 240554 | 0.51% | 726 |
| chr22 | 630640 | 1.24% | 1973 |
| chrX | 137610 | 0.09% | 439 |
| chrY | 3092 | 0.01% | 12 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 52168 | 125 | 3594 | 320.05 | 262 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF657VHK.bed.gz | 1.03 MB | bf40913df90c6cc3dbc789cd5e434118 |
| ENCFF657VHK.tabix.bed.gz | 518.74 KB | 4dd1a3e103eebd753dc1ae3fdcb3c830 |
| ENCFF657VHK.tabix.bed.gz.tbi | 152.56 KB | 59b73cd4f31a062ea24d2595e81039fa |
| genomic_resource.yaml | 3.66 KB | 7eb8f02db56a560a7e316c2bf9683494 |
| statistics/ |