Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:59:33 GMT 2023 |
| BAM file: | SRX7354228.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): | 44,902,147 / 44,860,642 |
| Number of aligned pairs (without duplicates): | 44,840,145 |
| Total number of alignments: | 95,210,306 |
| Number of secondary alignments: | 5,447,517 |
| Number of non-unique alignments: | 8,989,643 |
| Aligned to genes: | 75,360,413 |
| Ambiguous alignments: | 257,877 |
| No feature assigned: | 10,170,501 |
| Missing chromosome in annotation: | 431,872 |
| Not aligned: | 690,225 |
Reads genomic origin
| Exonic: | 75,360,413 / 88.11% |
| Intronic: | 6,511,971 / 7.61% |
| Intergenic: | 3,658,530 / 4.28% |
| Intronic/intergenic overlapping exon: | 3,640,492 / 4.26% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 23,212,085 |
| ACCT | 5.43% |
| AGGT | 4.63% |
| TCCT | 3.55% |
| ATCT | 3.45% |
| GCCT | 3.38% |
| AGGA | 3.32% |
| AGCT | 2.72% |
| CCCT | 2.53% |
| AGGC | 2.4% |
| TTCT | 2.05% |
| AGAT | 2% |

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