Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:19:59 GMT 2023 |
| BAM file: | SRX7354180.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): | 31,556,184 / 31,538,928 |
| Number of aligned pairs (without duplicates): | 31,535,627 |
| Total number of alignments: | 67,075,290 |
| Number of secondary alignments: | 3,980,178 |
| Number of non-unique alignments: | 6,581,649 |
| Aligned to genes: | 52,544,695 |
| Ambiguous alignments: | 190,639 |
| No feature assigned: | 7,484,759 |
| Missing chromosome in annotation: | 273,548 |
| Not aligned: | 2,198,286 |
Reads genomic origin
| Exonic: | 52,544,695 / 87.53% |
| Intronic: | 5,401,780 / 9% |
| Intergenic: | 2,082,979 / 3.47% |
| Intronic/intergenic overlapping exon: | 2,081,688 / 3.47% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 18,351,268 |
| ACCT | 5.35% |
| AGGT | 4.73% |
| AGGA | 3.64% |
| ATCT | 3.47% |
| TCCT | 3.34% |
| GCCT | 3.29% |
| AGCT | 2.82% |
| CCCT | 2.45% |
| AGGC | 2.42% |
| AGAT | 2.33% |
| TTCT | 2.11% |

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