Input data and parameters
Input
| Analysis date: | Wed Apr 27 19:35:55 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): | 19,638,224 / 19,400,291 |
| Number of aligned pairs (without duplicates): | 17,448,415 |
| Total number of alignments: | 41,576,869 |
| Number of secondary alignments: | 2,538,354 |
| Number of non-unique alignments: | 4,014,499 |
| Aligned to genes: | 33,552,491 |
| Ambiguous alignments: | 319,971 |
| No feature assigned: | 3,689,669 |
| Missing chromosome in annotation: | 239 |
| Not aligned: | 1,681,519 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 33,552,491 / 90.09% |
| Intronic: | 2,504,852 / 6.73% |
| Intergenic: | 1,184,817 / 3.18% |
| Intronic/intergenic overlapping exon: | 846,106 / 2.27% |
Transcript coverage profile
| 5' bias: | 0.67 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.58 |
Junction analysis
| Reads at junctions: | 21,301,122 |
| AGGT | 4.43% |
| ACCT | 4.35% |
| AGGA | 3.51% |
| AGGG | 3.11% |
| TCCT | 2.92% |
| CCCT | 2.86% |
| AGCT | 2.84% |
| AGAT | 2.57% |
| AGAA | 2.46% |
| ATCT | 2.38% |
| AGGC | 2.34% |
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