Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:05:23 GMT 2023 |
| BAM file: | SRX7354374.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): | 52,753,753 / 52,708,450 |
| Number of aligned pairs (without duplicates): | 52,702,661 |
| Total number of alignments: | 112,225,788 |
| Number of secondary alignments: | 6,763,585 |
| Number of non-unique alignments: | 11,409,808 |
| Aligned to genes: | 86,304,505 |
| Ambiguous alignments: | 313,791 |
| No feature assigned: | 13,818,934 |
| Missing chromosome in annotation: | 378,750 |
| Not aligned: | 5,949,749 |
Reads genomic origin
| Exonic: | 86,304,505 / 86.2% |
| Intronic: | 9,343,897 / 9.33% |
| Intergenic: | 4,475,037 / 4.47% |
| Intronic/intergenic overlapping exon: | 3,486,704 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.74 |
Junction analysis
| Reads at junctions: | 28,622,176 |
| ACCT | 5.36% |
| AGGT | 4.63% |
| ATCT | 3.61% |
| AGGA | 3.56% |
| TCCT | 3.34% |
| GCCT | 3.19% |
| AGCT | 2.72% |
| AGGC | 2.37% |
| CCCT | 2.33% |
| AGAT | 2.27% |
| TTCT | 2.2% |

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