Resource
| Id | Histone_ChIP-seq/ENCSR797IXN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR797IXN [biosample_summary="Homo sapiens layer of hippocampus tissue male adult (73 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (73 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN423NFY|/analyses/ENCAN423NFY/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF863LPA|/files/ENCFF863LPA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18901218 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 {ENCFF863LPA|/files/ENCFF863LPA/} processed by ChIP-seq ENCODE3 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 redacted alignments file {ENCFF863LPA|/files/ENCFF863LPA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.00. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR797IXN | float |
Histone_ChIP-seq_ENCSR797IXN |
Histone_ChIP-seq ENCSR797IXN [biosample_summary="Homo sapiens layer of hippocampus tissue male adult (73 years)" and target="H3K4me1"]
|
 |
[1.77, 19.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 90716124 | 2.82% | 95908 |
| chr1 | 9446818 | 3.79% | 9578 |
| chr2 | 7136727 | 2.95% | 7631 |
| chr3 | 5535136 | 2.79% | 6107 |
| chr4 | 3509836 | 1.85% | 3951 |
| chr5 | 4926174 | 2.71% | 5368 |
| chr6 | 4960408 | 2.90% | 5472 |
| chr7 | 4247926 | 2.67% | 4738 |
| chr8 | 3502113 | 2.41% | 3945 |
| chr9 | 4666300 | 3.37% | 4803 |
| chr10 | 5158809 | 3.86% | 5198 |
| chr11 | 5818792 | 4.31% | 5796 |
| chr12 | 3936104 | 2.95% | 4231 |
| chr13 | 2073769 | 1.81% | 2378 |
| chr14 | 3232654 | 3.02% | 3422 |
| chr15 | 3244571 | 3.18% | 3386 |
| chr16 | 3159295 | 3.50% | 3300 |
| chr17 | 4752384 | 5.71% | 4620 |
| chr18 | 1920899 | 2.39% | 2112 |
| chr19 | 2966157 | 5.06% | 3065 |
| chr20 | 2718613 | 4.22% | 2730 |
| chr21 | 975337 | 2.09% | 1084 |
| chr22 | 2118740 | 4.17% | 2035 |
| chrX | 692898 | 0.44% | 931 |
| chrY | 15664 | 0.03% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 95908 | 265 | 18036 | 945.87 | 742 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF123QQE.bed.gz | 1.93 MB | 1c65985635ab54a7587633311c4df2b1 |
| ENCFF123QQE.tabix.bed.gz | 971.47 KB | 4283844e4a891ac9624adfd301dc960a |
| ENCFF123QQE.tabix.bed.gz.tbi | 293.27 KB | 354a8addb063b3c0b13c1c451764ecbc |
| genomic_resource.yaml | 3.29 KB | 8fe721f6033c68820c5dc6efb2a55e11 |
| statistics/ |