Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:16:33 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): | 20,799,690 / 20,781,980 |
| Number of aligned pairs (without duplicates): | 19,191,138 |
| Total number of alignments: | 48,457,315 |
| Number of secondary alignments: | 6,875,645 |
| Number of non-unique alignments: | 9,849,799 |
| Aligned to genes: | 34,372,582 |
| Ambiguous alignments: | 260,455 |
| No feature assigned: | 3,974,407 |
| Missing chromosome in annotation: | 72 |
| Not aligned: | 1,051,878 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 34,372,582 / 89.64% |
| Intronic: | 1,757,524 / 4.58% |
| Intergenic: | 2,216,883 / 5.78% |
| Intronic/intergenic overlapping exon: | 719,239 / 1.88% |
Transcript coverage profile
| 5' bias: | 0.67 |
| 3' bias: | 0.33 |
| 5'-3' bias: | 1.45 |
Junction analysis
| Reads at junctions: | 23,741,627 |
| ACCT | 4.73% |
| AGGT | 4.36% |
| TCCT | 3.44% |
| AGCT | 3.4% |
| ATCT | 3.36% |
| AGGA | 3.05% |
| GCCT | 3.03% |
| AGGG | 3.02% |
| AGGC | 2.96% |
| CCCT | 2.33% |
| AGAT | 2.12% |
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