Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:03:03 GMT 2023 |
| BAM file: | SRX7354321.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): | 42,420,841 / 42,397,165 |
| Number of aligned pairs (without duplicates): | 42,388,957 |
| Total number of alignments: | 91,580,762 |
| Number of secondary alignments: | 6,762,756 |
| Number of non-unique alignments: | 10,660,394 |
| Aligned to genes: | 72,587,512 |
| Ambiguous alignments: | 254,206 |
| No feature assigned: | 7,356,937 |
| Missing chromosome in annotation: | 721,713 |
| Not aligned: | 3,302,606 |
Reads genomic origin
| Exonic: | 72,587,512 / 90.8% |
| Intronic: | 4,097,279 / 5.13% |
| Intergenic: | 3,259,658 / 4.08% |
| Intronic/intergenic overlapping exon: | 3,424,818 / 4.28% |
Transcript coverage profile
| 5' bias: | 0.06 |
| 3' bias: | 0.08 |
| 5'-3' bias: | 2.29 |
Junction analysis
| Reads at junctions: | 21,388,301 |
| ACCT | 5.86% |
| TCCT | 4.92% |
| ATCT | 4.68% |
| AGGT | 4.22% |
| CCCT | 3.67% |
| AGGA | 2.94% |
| GCCT | 2.44% |
| AGGC | 2.29% |
| TCCC | 2.28% |
| AGAC | 2.17% |
| CCCA | 2.02% |

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