Input data and parameters
Input
| Analysis date: | Tue Oct 31 17:40:58 GMT 2023 |
| BAM file: | SRX7354394.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): | 35,968,400 / 35,877,814 |
| Number of aligned pairs (without duplicates): | 35,830,916 |
| Total number of alignments: | 77,017,935 |
| Number of secondary alignments: | 5,171,721 |
| Number of non-unique alignments: | 8,424,568 |
| Aligned to genes: | 61,166,382 |
| Ambiguous alignments: | 215,708 |
| No feature assigned: | 6,728,245 |
| Missing chromosome in annotation: | 483,032 |
| Not aligned: | 6,342,294 |
Reads genomic origin
| Exonic: | 61,166,382 / 90.09% |
| Intronic: | 3,571,791 / 5.26% |
| Intergenic: | 3,156,454 / 4.65% |
| Intronic/intergenic overlapping exon: | 2,862,813 / 4.22% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 20,547,149 |
| ACCT | 5.52% |
| TCCT | 4.63% |
| ATCT | 4.32% |
| AGGT | 4.29% |
| GCCT | 3.54% |
| AGGA | 2.89% |
| CCCT | 2.63% |
| AGCT | 2.38% |
| AGGC | 2.24% |
| TTCT | 2.23% |
| TCCC | 2.17% |

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