Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:00:21 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): | 23,011,732 / 22,733,617 |
| Number of aligned pairs (without duplicates): | 20,735,972 |
| Total number of alignments: | 48,635,772 |
| Number of secondary alignments: | 2,890,423 |
| Number of non-unique alignments: | 4,601,142 |
| Aligned to genes: | 39,103,662 |
| Ambiguous alignments: | 352,759 |
| No feature assigned: | 4,577,916 |
| Missing chromosome in annotation: | 293 |
| Not aligned: | 1,808,371 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 39,103,662 / 89.52% |
| Intronic: | 3,240,596 / 7.42% |
| Intergenic: | 1,337,320 / 3.06% |
| Intronic/intergenic overlapping exon: | 971,103 / 2.22% |
Transcript coverage profile
| 5' bias: | 0.64 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.61 |
Junction analysis
| Reads at junctions: | 24,666,458 |
| AGGT | 4.53% |
| ACCT | 4.4% |
| AGGA | 3.64% |
| AGGG | 3.01% |
| TCCT | 2.94% |
| AGCT | 2.86% |
| CCCT | 2.68% |
| AGAT | 2.59% |
| AGAA | 2.5% |
| ATCT | 2.41% |
| AGGC | 2.39% |
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