Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:09:40 GMT 2023 |
| BAM file: | SRX7354198.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): | 38,215,094 / 38,192,852 |
| Number of aligned pairs (without duplicates): | 38,190,131 |
| Total number of alignments: | 81,210,745 |
| Number of secondary alignments: | 4,802,799 |
| Number of non-unique alignments: | 8,040,508 |
| Aligned to genes: | 64,526,635 |
| Ambiguous alignments: | 215,579 |
| No feature assigned: | 8,087,077 |
| Missing chromosome in annotation: | 340,946 |
| Not aligned: | 3,218,298 |
Reads genomic origin
| Exonic: | 64,526,635 / 88.86% |
| Intronic: | 5,282,114 / 7.27% |
| Intergenic: | 2,804,963 / 3.86% |
| Intronic/intergenic overlapping exon: | 2,364,879 / 3.26% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2.12 |
Junction analysis
| Reads at junctions: | 20,443,792 |
| ACCT | 5.45% |
| AGGT | 4.57% |
| ATCT | 3.8% |
| TCCT | 3.46% |
| AGGA | 3.37% |
| GCCT | 3.25% |
| AGCT | 2.72% |
| TTCT | 2.47% |
| CCCT | 2.43% |
| AGGC | 2.3% |
| AGAT | 2.19% |

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