Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:40:14 GMT 2023 |
| BAM file: | SRX7354113.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): | 37,921,046 / 37,905,083 |
| Number of aligned pairs (without duplicates): | 37,901,715 |
| Total number of alignments: | 80,826,523 |
| Number of secondary alignments: | 5,000,394 |
| Number of non-unique alignments: | 7,909,621 |
| Aligned to genes: | 63,052,001 |
| Ambiguous alignments: | 210,791 |
| No feature assigned: | 9,131,213 |
| Missing chromosome in annotation: | 522,897 |
| Not aligned: | 1,786,247 |
Reads genomic origin
| Exonic: | 63,052,001 / 87.35% |
| Intronic: | 6,706,362 / 9.29% |
| Intergenic: | 2,424,851 / 3.36% |
| Intronic/intergenic overlapping exon: | 2,277,998 / 3.16% |
Transcript coverage profile
| 5' bias: | 0.46 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.09 |
Junction analysis
| Reads at junctions: | 21,316,452 |
| ACCT | 5.58% |
| AGGT | 4.68% |
| ATCT | 3.51% |
| AGGA | 3.46% |
| TCCT | 3.22% |
| GCCT | 3.22% |
| AGCT | 2.79% |
| CCCT | 2.45% |
| AGGC | 2.41% |
| AGAT | 2.36% |
| TTCT | 2.1% |

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