Resource
| Id | Histone_ChIP-seq/ENCSR758GMX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR758GMX [biosample_summary="Homo sapiens hepatocyte originated from H9" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (5 days) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN849OYG|/analyses/ENCAN849OYG/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF863OUQ|/files/ENCFF863OUQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 34865437 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 unfiltered alignments file {ENCFF045PWH|/files/ENCFF045PWH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 34865437 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF824QCO|/files/ENCFF824QCO/} 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 {ENCFF824QCO|/files/ENCFF824QCO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.54. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR758GMX | float |
Histone_ChIP-seq_ENCSR758GMX |
Histone_ChIP-seq ENCSR758GMX [biosample_summary="Homo sapiens hepatocyte originated from H9" and target="H3K9me3"]
|
 |
[1.33, 8.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14700500 | 0.46% | 22071 |
| chr1 | 815133 | 0.33% | 1303 |
| chr1_KI270709v1_random | 5625 | 8.41% | 11 |
| chr2 | 847547 | 0.35% | 1394 |
| chr2_KI270716v1_random | 1527 | 0.99% | 3 |
| chr3 | 584182 | 0.29% | 1009 |
| chr3_GL000221v1_random | 406 | 0.26% | 1 |
| chr4 | 657728 | 0.35% | 1007 |
| chr4_GL000008v2_random | 4544 | 2.17% | 2 |
| chr5 | 860325 | 0.47% | 1364 |
| chr5_GL000208v1_random | 11422 | 12.32% | 16 |
| chr6 | 546737 | 0.32% | 923 |
| chr7 | 978340 | 0.61% | 1362 |
| chr8 | 591021 | 0.41% | 995 |
| chr9 | 471418 | 0.34% | 722 |
| chr9_KI270719v1_random | 2189 | 1.24% | 6 |
| chr9_KI270720v1_random | 818 | 2.09% | 2 |
| chr10 | 670790 | 0.50% | 1056 |
| chr11 | 554243 | 0.41% | 927 |
| chr12 | 671641 | 0.50% | 1007 |
| chr13 | 278388 | 0.24% | 465 |
| chr14 | 396359 | 0.37% | 667 |
| chr14_GL000009v2_random | 664 | 0.33% | 1 |
| chr14_GL000194v1_random | 1430 | 0.75% | 1 |
| chr14_GL000225v1_random | 22615 | 10.71% | 33 |
| chr14_KI270722v1_random | 15405 | 7.94% | 16 |
| chr14_KI270723v1_random | 372 | 0.98% | 1 |
| chr14_KI270724v1_random | 2442 | 6.17% | 3 |
| chr14_KI270725v1_random | 1804 | 1.04% | 4 |
| chr15 | 422908 | 0.41% | 650 |
| chr16 | 379176 | 0.42% | 563 |
| chr17 | 233217 | 0.28% | 378 |
| chr17_GL000205v2_random | 35369 | 19.06% | 24 |
| chr17_KI270729v1_random | 31116 | 11.08% | 44 |
| chr17_KI270730v1_random | 4110 | 3.65% | 7 |
| chr18 | 214839 | 0.27% | 350 |
| chr19 | 2414041 | 4.12% | 2477 |
| chr20 | 253251 | 0.39% | 421 |
| chr21 | 409378 | 0.88% | 556 |
| chr22 | 135265 | 0.27% | 231 |
| chr22_KI270732v1_random | 3113 | 7.49% | 6 |
| chr22_KI270733v1_random | 3869 | 2.15% | 5 |
| chr22_KI270735v1_random | 5272 | 12.31% | 10 |
| chr22_KI270736v1_random | 8388 | 4.61% | 11 |
| chr22_KI270738v1_random | 5386 | 5.42% | 10 |
| chrM | 11419 | 68.92% | 7 |
| chrUn_GL000195v1 | 315 | 0.17% | 1 |
| chrUn_GL000214v1 | 409 | 0.30% | 1 |
| chrUn_GL000216v2 | 33800 | 19.14% | 32 |
| chrUn_GL000218v1 | 2087 | 1.30% | 5 |
| chrUn_GL000219v1 | 4579 | 2.56% | 4 |
| chrUn_GL000220v1 | 362 | 0.22% | 1 |
| chrUn_GL000224v1 | 10905 | 6.07% | 12 |
| chrUn_KI270320v1 | 582 | 13.18% | 1 |
| chrUn_KI270333v1 | 318 | 11.78% | 1 |
| chrUn_KI270337v1 | 480 | 42.82% | 1 |
| chrUn_KI270435v1 | 9935 | 10.68% | 8 |
| chrUn_KI270438v1 | 23940 | 21.28% | 29 |
| chrUn_KI270442v1 | 93445 | 23.83% | 101 |
| chrUn_KI270448v1 | 3155 | 39.48% | 4 |
| chrUn_KI270465v1 | 415 | 23.39% | 1 |
| chrUn_KI270466v1 | 879 | 71.29% | 2 |
| chrUn_KI270467v1 | 1523 | 38.85% | 1 |
| chrUn_KI270468v1 | 1800 | 44.39% | 2 |
| chrUn_KI270507v1 | 2855 | 53.33% | 4 |
| chrUn_KI270508v1 | 970 | 49.72% | 1 |
| chrUn_KI270509v1 | 1467 | 63.29% | 2 |
| chrUn_KI270510v1 | 629 | 26.05% | 2 |
| chrUn_KI270511v1 | 4532 | 55.76% | 1 |
| chrUn_KI270512v1 | 973 | 4.29% | 2 |
| chrUn_KI270515v1 | 4269 | 67.11% | 3 |
| chrUn_KI270516v1 | 667 | 51.31% | 1 |
| chrUn_KI270517v1 | 1615 | 49.65% | 1 |
| chrUn_KI270518v1 | 1500 | 68.62% | 1 |
| chrUn_KI270519v1 | 13318 | 9.64% | 27 |
| chrUn_KI270538v1 | 23269 | 25.48% | 26 |
| chrUn_KI270584v1 | 2891 | 64.06% | 4 |
| chrUn_KI270587v1 | 1529 | 51.50% | 1 |
| chrUn_KI270588v1 | 1853 | 30.09% | 3 |
| chrUn_KI270589v1 | 3585 | 8.06% | 2 |
| chrUn_KI270590v1 | 1947 | 41.56% | 2 |
| chrUn_KI270591v1 | 3553 | 61.30% | 4 |
| chrUn_KI270742v1 | 755 | 0.40% | 2 |
| chrUn_KI270744v1 | 3795 | 2.25% | 4 |
| chrUn_KI270746v1 | 6307 | 9.49% | 11 |
| chrUn_KI270749v1 | 696 | 0.44% | 1 |
| chrUn_KI270750v1 | 12237 | 8.22% | 19 |
| chrUn_KI270751v1 | 9641 | 6.40% | 18 |
| chrUn_KI270754v1 | 469 | 1.17% | 1 |
| chrUn_KI270756v1 | 364 | 0.46% | 1 |
| chrUn_KI270757v1 | 12478 | 17.51% | 15 |
| chrX | 800206 | 0.51% | 1616 |
| chrY | 27969 | 0.05% | 38 |
| 3274 contigs with no values (122764000 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 22071 | 210 | 13133 | 666.06 | 515 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF136JCP.bed.gz | 449.17 KB | ea6083cc243aadbe68803ef0d6e8f99e |
| ENCFF136JCP.tabix.bed.gz | 224.7 KB | eaf9be3eb61bfbc082044abcc77d6738 |
| ENCFF136JCP.tabix.bed.gz.tbi | 118.8 KB | 45ad5465adf8ad8269a2ae771a0c4f38 |
| genomic_resource.yaml | 3.71 KB | a9bed58c08250c427bfded0f8165375f |
| statistics/ |