Resource
| Id | Histone_ChIP-seq/ENCSR730FLZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR730FLZ [biosample_summary="Homo sapiens ES-I3" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN689USM|/analyses/ENCAN689USM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF034HOR|/files/ENCFF034HOR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 22483470 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 {ENCFF117URS|/files/ENCFF117URS/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13475854 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 {ENCFF034HOR|/files/ENCFF034HOR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF034HOR|/files/ENCFF034HOR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.82. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR730FLZ | float |
Histone_ChIP-seq_ENCSR730FLZ |
Histone_ChIP-seq ENCSR730FLZ [biosample_summary="Homo sapiens ES-I3" and target="H3K4me1"]
|
 |
[1.66, 13.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 94858056 | 2.95% | 159350 |
| chr1 | 8856575 | 3.56% | 14376 |
| chr1_KI270713v1_random | 350 | 0.86% | 1 |
| chr2 | 7548942 | 3.12% | 12725 |
| chr3 | 6947252 | 3.50% | 11560 |
| chr4 | 4953729 | 2.60% | 8446 |
| chr5 | 5692120 | 3.14% | 9483 |
| chr6 | 5852097 | 3.43% | 9784 |
| chr7 | 4674904 | 2.93% | 7999 |
| chr8 | 4475341 | 3.08% | 7510 |
| chr9 | 3957615 | 2.86% | 6661 |
| chr10 | 4380242 | 3.27% | 7341 |
| chr11 | 4780265 | 3.54% | 7924 |
| chr12 | 4542256 | 3.41% | 7640 |
| chr13 | 2614570 | 2.29% | 4543 |
| chr14 | 2957009 | 2.76% | 5032 |
| chr15 | 3074544 | 3.01% | 5023 |
| chr16 | 2659138 | 2.94% | 4601 |
| chr17 | 4060201 | 4.88% | 6480 |
| chr17_GL000205v2_random | 1413 | 0.76% | 3 |
| chr18 | 2386440 | 2.97% | 4068 |
| chr19 | 1524973 | 2.60% | 2895 |
| chr20 | 2316483 | 3.59% | 3997 |
| chr21 | 865369 | 1.85% | 1527 |
| chr22 | 1611970 | 3.17% | 2719 |
| chr22_KI270733v1_random | 1110 | 0.62% | 3 |
| chrUn_GL000195v1 | 2573 | 1.41% | 2 |
| chrX | 4120575 | 2.64% | 7007 |
| 3339 contigs with no values (185715496 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 159350 | 195 | 8491 | 595.28 | 483 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF327XLP.bed.gz | 3.38 MB | bce0d2db834e560834896d7b24549e68 |
| ENCFF327XLP.tabix.bed.gz | 1.59 MB | c8d04c5398b02471634129ae48f004ca |
| ENCFF327XLP.tabix.bed.gz.tbi | 467.37 KB | 59cd6ab2fd4d67a6db385144809b780a |
| genomic_resource.yaml | 3.67 KB | 5b5631dbceb821f0b7c692d639fc6c0a |
| statistics/ |