Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:15:00 GMT 2023 |
| BAM file: | SRX7354252.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): | 35,471,962 / 35,452,961 |
| Number of aligned pairs (without duplicates): | 35,448,832 |
| Total number of alignments: | 75,473,531 |
| Number of secondary alignments: | 4,548,608 |
| Number of non-unique alignments: | 6,852,702 |
| Aligned to genes: | 59,821,288 |
| Ambiguous alignments: | 230,140 |
| No feature assigned: | 7,929,610 |
| Missing chromosome in annotation: | 639,791 |
| Not aligned: | 1,912,663 |
Reads genomic origin
| Exonic: | 59,821,288 / 88.3% |
| Intronic: | 5,414,463 / 7.99% |
| Intergenic: | 2,515,147 / 3.71% |
| Intronic/intergenic overlapping exon: | 2,360,782 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.04 |
Junction analysis
| Reads at junctions: | 21,408,486 |
| ACCT | 5.57% |
| AGGT | 4.71% |
| ATCT | 3.55% |
| AGGA | 3.5% |
| TCCT | 3.47% |
| GCCT | 3.32% |
| AGCT | 2.63% |
| CCCT | 2.37% |
| AGGC | 2.37% |
| AGAT | 2.17% |
| TTCT | 2.16% |

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