Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:10:34 GMT 2023 |
| BAM file: | SRX7354287.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): | 41,179,078 / 41,163,683 |
| Number of aligned pairs (without duplicates): | 41,160,538 |
| Total number of alignments: | 88,066,736 |
| Number of secondary alignments: | 5,723,975 |
| Number of non-unique alignments: | 9,066,266 |
| Aligned to genes: | 65,609,315 |
| Ambiguous alignments: | 244,345 |
| No feature assigned: | 12,500,091 |
| Missing chromosome in annotation: | 646,719 |
| Not aligned: | 2,350,697 |
Reads genomic origin
| Exonic: | 65,609,315 / 84% |
| Intronic: | 7,006,116 / 8.97% |
| Intergenic: | 5,493,975 / 7.03% |
| Intronic/intergenic overlapping exon: | 2,781,279 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.51 |
| 3' bias: | 0.26 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 23,410,277 |
| ACCT | 5.15% |
| AGGT | 4.77% |
| ATCT | 3.54% |
| AGGA | 3.53% |
| TCCT | 3.49% |
| GCCT | 3.27% |
| AGCT | 2.78% |
| CCCT | 2.71% |
| AGGC | 2.44% |
| AGAT | 2.19% |
| TTCT | 2.18% |
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