Input data and parameters
Input
| Analysis date: | Wed Apr 27 19:56:18 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): | 23,013,618 / 22,710,420 |
| Number of aligned pairs (without duplicates): | 19,857,866 |
| Total number of alignments: | 48,632,676 |
| Number of secondary alignments: | 2,908,638 |
| Number of non-unique alignments: | 4,597,542 |
| Aligned to genes: | 39,481,459 |
| Ambiguous alignments: | 370,092 |
| No feature assigned: | 4,183,236 |
| Missing chromosome in annotation: | 347 |
| Not aligned: | 2,021,978 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 39,481,459 / 90.42% |
| Intronic: | 2,939,120 / 6.73% |
| Intergenic: | 1,244,116 / 2.85% |
| Intronic/intergenic overlapping exon: | 1,081,657 / 2.48% |
Transcript coverage profile
| 5' bias: | 0.69 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.46 |
Junction analysis
| Reads at junctions: | 25,136,813 |
| AGGT | 4.43% |
| ACCT | 4.32% |
| AGGA | 3.6% |
| AGGG | 3.06% |
| CCCT | 2.94% |
| TCCT | 2.94% |
| AGCT | 2.77% |
| AGAA | 2.62% |
| AGAT | 2.56% |
| AGGC | 2.39% |
| ATCT | 2.34% |
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