Resource
| Id | Histone_ChIP-seq/ENCSR485ZKB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR485ZKB [biosample_summary="Homo sapiens UCSF-4" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN873UHL|/analyses/ENCAN873UHL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF358EIU|/files/ENCFF358EIU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 20733279 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 redacted alignments file {ENCFF018OSY|/files/ENCFF018OSY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15013331 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 {ENCFF358EIU|/files/ENCFF358EIU/} processed by ChIP-seq ENCODE3 GRCh38 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 redacted alignments file {ENCFF358EIU|/files/ENCFF358EIU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR485ZKB | float |
Histone_ChIP-seq_ENCSR485ZKB |
Histone_ChIP-seq ENCSR485ZKB [biosample_summary="Homo sapiens UCSF-4" and target="H3K27me3"]
|
 |
[1.19, 38.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 42694115 | 1.33% | 60789 |
| chr1 | 3055793 | 1.23% | 3945 |
| chr1_KI270706v1_random | 607 | 0.35% | 2 |
| chr1_KI270707v1_random | 329 | 1.03% | 1 |
| chr1_KI270709v1_random | 2810 | 4.20% | 6 |
| chr1_KI270712v1_random | 887 | 0.50% | 3 |
| chr1_KI270713v1_random | 2073 | 5.09% | 2 |
| chr2 | 2365738 | 0.98% | 2996 |
| chr3 | 1363580 | 0.69% | 2109 |
| chr4 | 1666692 | 0.88% | 2236 |
| chr4_GL000008v2_random | 4576 | 2.18% | 2 |
| chr5 | 1697350 | 0.93% | 2232 |
| chr5_GL000208v1_random | 3815 | 4.12% | 7 |
| chr6 | 1623818 | 0.95% | 2076 |
| chr7 | 2136379 | 1.34% | 2865 |
| chr8 | 1718028 | 1.18% | 2352 |
| chr9 | 1485607 | 1.07% | 1959 |
| chr9_KI270718v1_random | 460 | 1.21% | 1 |
| chr9_KI270719v1_random | 5315 | 3.01% | 12 |
| chr9_KI270720v1_random | 2163 | 5.54% | 4 |
| chr10 | 1810719 | 1.35% | 2295 |
| chr11 | 2016966 | 1.49% | 2697 |
| chr12 | 1929998 | 1.45% | 2260 |
| chr13 | 801691 | 0.70% | 1122 |
| chr14 | 1207153 | 1.13% | 1714 |
| chr14_GL000009v2_random | 2520 | 1.25% | 7 |
| chr14_GL000194v1_random | 8346 | 4.36% | 13 |
| chr14_GL000225v1_random | 76859 | 36.40% | 89 |
| chr14_KI270722v1_random | 10394 | 5.36% | 18 |
| chr14_KI270723v1_random | 4713 | 12.37% | 10 |
| chr14_KI270724v1_random | 1824 | 4.61% | 4 |
| chr14_KI270725v1_random | 1679 | 0.97% | 5 |
| chr15 | 1018456 | 1.00% | 1295 |
| chr16 | 1261636 | 1.40% | 1730 |
| chr16_KI270728v1_random | 1411 | 0.08% | 5 |
| chr17 | 1767454 | 2.12% | 1961 |
| chr17_GL000205v2_random | 44300 | 23.87% | 36 |
| chr17_KI270729v1_random | 8856 | 3.15% | 13 |
| chr17_KI270730v1_random | 11316 | 10.05% | 21 |
| chr18 | 594517 | 0.74% | 859 |
| chr19 | 2383117 | 4.07% | 3683 |
| chr20 | 1240736 | 1.93% | 1801 |
| chr21 | 506555 | 1.08% | 811 |
| chr22 | 1201639 | 2.36% | 1637 |
| chr22_KI270732v1_random | 1839 | 4.43% | 3 |
| chr22_KI270733v1_random | 4098 | 2.28% | 12 |
| chr22_KI270735v1_random | 5078 | 11.86% | 6 |
| chr22_KI270736v1_random | 19350 | 10.64% | 28 |
| chr22_KI270738v1_random | 1573 | 1.58% | 4 |
| chrM | 841 | 5.08% | 2 |
| chrUn_GL000214v1 | 3504 | 2.54% | 9 |
| chrUn_GL000216v2 | 14263 | 8.08% | 31 |
| chrUn_GL000218v1 | 9438 | 5.86% | 24 |
| chrUn_GL000219v1 | 18845 | 10.52% | 26 |
| chrUn_GL000220v1 | 591 | 0.37% | 2 |
| chrUn_GL000224v1 | 13682 | 7.61% | 27 |
| chrUn_KI270330v1 | 267 | 16.16% | 1 |
| chrUn_KI270333v1 | 246 | 9.11% | 1 |
| chrUn_KI270382v1 | 409 | 9.70% | 1 |
| chrUn_KI270435v1 | 2844 | 3.06% | 5 |
| chrUn_KI270438v1 | 9088 | 8.08% | 16 |
| chrUn_KI270442v1 | 74558 | 19.02% | 118 |
| chrUn_KI270448v1 | 381 | 4.77% | 1 |
| chrUn_KI270467v1 | 215 | 5.48% | 1 |
| chrUn_KI270468v1 | 286 | 7.05% | 1 |
| chrUn_KI270507v1 | 859 | 16.05% | 2 |
| chrUn_KI270510v1 | 207 | 8.57% | 1 |
| chrUn_KI270511v1 | 598 | 7.36% | 2 |
| chrUn_KI270512v1 | 1599 | 7.05% | 2 |
| chrUn_KI270518v1 | 418 | 19.12% | 1 |
| chrUn_KI270519v1 | 5061 | 3.66% | 9 |
| chrUn_KI270538v1 | 2692 | 2.95% | 6 |
| chrUn_KI270584v1 | 658 | 14.58% | 2 |
| chrUn_KI270588v1 | 857 | 13.92% | 2 |
| chrUn_KI270589v1 | 2579 | 5.80% | 2 |
| chrUn_KI270590v1 | 1411 | 30.12% | 3 |
| chrUn_KI270591v1 | 1129 | 19.48% | 2 |
| chrUn_KI270742v1 | 658 | 0.35% | 2 |
| chrUn_KI270743v1 | 1101 | 0.52% | 4 |
| chrUn_KI270744v1 | 5863 | 3.48% | 10 |
| chrUn_KI270746v1 | 1695 | 2.55% | 4 |
| chrUn_KI270747v1 | 2140 | 1.08% | 2 |
| chrUn_KI270749v1 | 1014 | 0.64% | 2 |
| chrUn_KI270750v1 | 1231 | 0.83% | 3 |
| chrUn_KI270751v1 | 4410 | 2.93% | 10 |
| chrUn_KI270753v1 | 583 | 0.93% | 1 |
| chrUn_KI270754v1 | 1837 | 4.57% | 6 |
| chrUn_KI270756v1 | 904 | 1.14% | 2 |
| chrUn_KI270757v1 | 3615 | 5.07% | 7 |
| chrX | 7392016 | 4.74% | 13439 |
| chrY | 28709 | 0.05% | 48 |
| 3276 contigs with no values (120469896 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 60789 | 170 | 65284 | 702.33 | 457 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF906DAU.bed.gz | 1.18 MB | 9c3eb59a2f997ccca2624cc8d7bd6799 |
| ENCFF906DAU.tabix.bed.gz | 603.35 KB | 24382e5468b80728eb9dabec883dfc77 |
| ENCFF906DAU.tabix.bed.gz.tbi | 238.18 KB | 5a0921e4c0037023f23abeb08c3b26b6 |
| genomic_resource.yaml | 3.71 KB | b554bb8c4350b904450781de5f3eaa48 |
| statistics/ |