Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:44:25 GMT 2023 |
| BAM file: | SRX7354183.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): | 36,392,574 / 36,380,480 |
| Number of aligned pairs (without duplicates): | 36,377,388 |
| Total number of alignments: | 78,111,554 |
| Number of secondary alignments: | 5,338,500 |
| Number of non-unique alignments: | 8,483,075 |
| Aligned to genes: | 57,184,622 |
| Ambiguous alignments: | 222,862 |
| No feature assigned: | 11,639,800 |
| Missing chromosome in annotation: | 581,195 |
| Not aligned: | 1,949,258 |
Reads genomic origin
| Exonic: | 57,184,622 / 83.09% |
| Intronic: | 7,322,000 / 10.64% |
| Intergenic: | 4,317,800 / 6.27% |
| Intronic/intergenic overlapping exon: | 2,388,646 / 3.47% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.63 |
Junction analysis
| Reads at junctions: | 21,481,595 |
| ACCT | 5.18% |
| AGGT | 4.67% |
| ATCT | 3.61% |
| TCCT | 3.49% |
| GCCT | 3.47% |
| AGGA | 3.36% |
| AGCT | 2.76% |
| CCCT | 2.73% |
| AGGC | 2.43% |
| TTCT | 2.19% |
| AGAT | 2.09% |

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