Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:31:10 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): | 19,683,023 / 19,669,307 |
| Number of aligned pairs (without duplicates): | 18,106,988 |
| Total number of alignments: | 46,335,718 |
| Number of secondary alignments: | 6,983,388 |
| Number of non-unique alignments: | 9,908,533 |
| Aligned to genes: | 32,192,411 |
| Ambiguous alignments: | 250,743 |
| No feature assigned: | 3,983,909 |
| Missing chromosome in annotation: | 122 |
| Not aligned: | 947,972 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 32,192,411 / 88.99% |
| Intronic: | 1,940,692 / 5.36% |
| Intergenic: | 2,043,217 / 5.65% |
| Intronic/intergenic overlapping exon: | 683,579 / 1.89% |
Transcript coverage profile
| 5' bias: | 0.67 |
| 3' bias: | 0.31 |
| 5'-3' bias: | 1.48 |
Junction analysis
| Reads at junctions: | 22,155,657 |
| ACCT | 4.7% |
| AGGT | 4.27% |
| ATCT | 3.44% |
| AGCT | 3.44% |
| TCCT | 3.42% |
| AGGG | 3.18% |
| GCCT | 3.13% |
| AGGC | 3.04% |
| AGGA | 2.94% |
| CCCT | 2.38% |
| AGAT | 2.06% |
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