Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:14:54 CST 2022 |
| BAM file: | /dev/stdin |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | /home/bayegy/Databases/transcriptome/references/mmu/GCF_000001635.27_GRCm39_genomic.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | non-strand-specific |
| Sorting performed: | no |
Summary
Reads alignment
| Number of mapped reads (left/right): | 20,747,769 / 20,700,578 |
| Number of aligned pairs (without duplicates): | 19,171,152 |
| Total number of alignments: | 46,682,199 |
| Number of secondary alignments: | 5,233,852 |
| Number of non-unique alignments: | 7,926,964 |
| Aligned to genes: | 34,097,009 |
| Ambiguous alignments: | 249,429 |
| No feature assigned: | 4,408,700 |
| Missing chromosome in annotation: | 97 |
| Not aligned: | 977,517 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 34,097,009 / 88.55% |
| Intronic: | 2,290,021 / 5.95% |
| Intergenic: | 2,118,679 / 5.5% |
| Intronic/intergenic overlapping exon: | 749,521 / 1.95% |
Transcript coverage profile
| 5' bias: | 0.65 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.39 |
Junction analysis
| Reads at junctions: | 24,148,556 |
| ACCT | 4.56% |
| AGGT | 4.22% |
| AGCT | 3.59% |
| ATCT | 3.43% |
| TCCT | 3.32% |
| AGGG | 3.09% |
| AGGA | 2.99% |
| GCCT | 2.89% |
| AGGC | 2.87% |
| CCCT | 2.26% |
| AGAT | 2.11% |
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