Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:45:11 GMT 2023 |
| BAM file: | SRX7354342.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.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: | strand-specific-reverse |
| Sorting performed: | yes |
Summary
Reads alignment
| Number of mapped reads (left/right): | 39,258,126 / 39,223,657 |
| Number of aligned pairs (without duplicates): | 39,217,100 |
| Total number of alignments: | 82,720,236 |
| Number of secondary alignments: | 4,238,453 |
| Number of non-unique alignments: | 7,101,497 |
| Aligned to genes: | 65,369,703 |
| Ambiguous alignments: | 216,867 |
| No feature assigned: | 9,789,173 |
| Missing chromosome in annotation: | 242,996 |
| Not aligned: | 9,131,441 |
Reads genomic origin
| Exonic: | 65,369,703 / 86.98% |
| Intronic: | 6,894,317 / 9.17% |
| Intergenic: | 2,894,856 / 3.85% |
| Intronic/intergenic overlapping exon: | 2,613,774 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 22,810,658 |
| ACCT | 5.32% |
| AGGT | 4.58% |
| AGGA | 3.6% |
| ATCT | 3.58% |
| TCCT | 3.33% |
| GCCT | 3.19% |
| AGCT | 2.85% |
| AGGC | 2.37% |
| AGAT | 2.37% |
| CCCT | 2.14% |
| TTCT | 2.13% |
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