Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:50:26 GMT 2023 |
| BAM file: | SRX7354352.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): | 44,298,364 / 44,234,181 |
| Number of aligned pairs (without duplicates): | 44,223,683 |
| Total number of alignments: | 95,914,859 |
| Number of secondary alignments: | 7,382,314 |
| Number of non-unique alignments: | 12,667,803 |
| Aligned to genes: | 73,658,809 |
| Ambiguous alignments: | 287,580 |
| No feature assigned: | 8,925,165 |
| Missing chromosome in annotation: | 375,502 |
| Not aligned: | 3,816,697 |
Reads genomic origin
| Exonic: | 73,658,809 / 89.19% |
| Intronic: | 5,536,302 / 6.7% |
| Intergenic: | 3,388,863 / 4.1% |
| Intronic/intergenic overlapping exon: | 3,360,899 / 4.07% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.78 |
Junction analysis
| Reads at junctions: | 22,470,791 |
| ACCT | 5.17% |
| AGGT | 4.54% |
| TCCT | 4.04% |
| ATCT | 3.93% |
| GCCT | 3.35% |
| AGGA | 3.26% |
| CCCT | 2.84% |
| AGCT | 2.49% |
| AGGC | 2.34% |
| TTCT | 2.21% |
| AGAT | 1.86% |

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