Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:41:47 GMT 2023 |
| BAM file: | SRX7354085.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): | 49,369,796 / 49,337,492 |
| Number of aligned pairs (without duplicates): | 49,331,759 |
| Total number of alignments: | 105,178,227 |
| Number of secondary alignments: | 6,470,939 |
| Number of non-unique alignments: | 10,879,826 |
| Aligned to genes: | 80,902,865 |
| Ambiguous alignments: | 270,739 |
| No feature assigned: | 12,700,796 |
| Missing chromosome in annotation: | 424,001 |
| Not aligned: | 7,091,938 |
Reads genomic origin
| Exonic: | 80,902,865 / 86.43% |
| Intronic: | 8,029,222 / 8.58% |
| Intergenic: | 4,671,574 / 4.99% |
| Intronic/intergenic overlapping exon: | 3,295,364 / 3.52% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.75 |
Junction analysis
| Reads at junctions: | 23,883,255 |
| ACCT | 5.38% |
| AGGT | 4.77% |
| AGGA | 3.58% |
| ATCT | 3.53% |
| TCCT | 3.39% |
| GCCT | 3.22% |
| AGCT | 2.75% |
| AGGC | 2.43% |
| CCCT | 2.36% |
| AGAT | 2.34% |
| TTCT | 2.25% |

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