Resource
| Id | Histone_ChIP-seq/ENCSR307OAJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR307OAJ [biosample_summary="Homo sapiens iPS DF 19.11" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN004MGL|/analyses/ENCAN004MGL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF980EDY|/files/ENCFF980EDY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19540402 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_not_compliant: Processed alignments file {ENCFF773ZEH|/files/ENCFF773ZEH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 20581752 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 alignments file {ENCFF773ZEH|/files/ENCFF773ZEH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF773ZEH|/files/ENCFF773ZEH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.59. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR307OAJ | float |
Histone_ChIP-seq_ENCSR307OAJ |
Histone_ChIP-seq ENCSR307OAJ [biosample_summary="Homo sapiens iPS DF 19.11" and target="H3K4me1"]
|
 |
[1.68, 20.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 66618328 | 2.07% | 220840 |
| chr1 | 6606087 | 2.65% | 21577 |
| chr1_KI270712v1_random | 1012 | 0.57% | 3 |
| chr1_KI270713v1_random | 307 | 0.75% | 1 |
| chr2 | 4625034 | 1.91% | 16183 |
| chr3 | 2969719 | 1.50% | 10785 |
| chr4 | 1933674 | 1.02% | 6887 |
| chr5 | 2648166 | 1.46% | 9437 |
| chr6 | 2723093 | 1.59% | 10072 |
| chr7 | 3187976 | 2.00% | 10734 |
| chr8 | 2604654 | 1.79% | 8849 |
| chr9 | 3400087 | 2.46% | 10863 |
| chr9_KI270718v1_random | 153 | 0.40% | 1 |
| chr10 | 3269571 | 2.44% | 11310 |
| chr11 | 4323497 | 3.20% | 13621 |
| chr12 | 2642833 | 1.98% | 9064 |
| chr13 | 1209689 | 1.06% | 4555 |
| chr14 | 2205358 | 2.06% | 7220 |
| chr14_GL000225v1_random | 740 | 0.35% | 3 |
| chr15 | 2297682 | 2.25% | 7954 |
| chr16 | 3455194 | 3.82% | 10635 |
| chr17 | 4753095 | 5.71% | 14054 |
| chr17_GL000205v2_random | 2468 | 1.33% | 9 |
| chr18 | 1142738 | 1.42% | 4441 |
| chr19 | 4174073 | 7.12% | 11873 |
| chr20 | 2493272 | 3.87% | 8098 |
| chr21 | 878198 | 1.88% | 2897 |
| chr22 | 2542272 | 5.00% | 7686 |
| chr22_KI270733v1_random | 1360 | 0.76% | 7 |
| chrUn_GL000195v1 | 388 | 0.21% | 2 |
| chrUn_GL000214v1 | 177 | 0.13% | 1 |
| chrUn_GL000216v2 | 122 | 0.07% | 1 |
| chrUn_GL000220v1 | 181 | 0.11% | 1 |
| chrUn_KI270442v1 | 415 | 0.11% | 3 |
| chrX | 521943 | 0.33% | 1997 |
| chrY | 3100 | 0.01% | 16 |
| 3331 contigs with no values (127194622 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 220840 | 120 | 5670 | 301.66 | 223 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF897KEO.bed.gz | 4.12 MB | 922f670bc28cd424ea1b11e6539dd31e |
| ENCFF897KEO.tabix.bed.gz | 2.07 MB | c97337d18612337c8bab212a8480395b |
| ENCFF897KEO.tabix.bed.gz.tbi | 420.09 KB | 64c3a493be226833c380404d434d68eb |
| genomic_resource.yaml | 3.69 KB | 426bedae6a9b693cdc6c428ec25ef4f1 |
| statistics/ |