Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:21:28 GMT 2023 |
| BAM file: | SRX7354148.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): | 28,838,728 / 28,820,203 |
| Number of aligned pairs (without duplicates): | 28,816,820 |
| Total number of alignments: | 61,366,141 |
| Number of secondary alignments: | 3,707,210 |
| Number of non-unique alignments: | 6,039,514 |
| Aligned to genes: | 47,425,420 |
| Ambiguous alignments: | 151,426 |
| No feature assigned: | 7,417,694 |
| Missing chromosome in annotation: | 332,087 |
| Not aligned: | 3,004,879 |
Reads genomic origin
| Exonic: | 47,425,420 / 86.47% |
| Intronic: | 5,020,951 / 9.16% |
| Intergenic: | 2,396,743 / 4.37% |
| Intronic/intergenic overlapping exon: | 1,863,526 / 3.4% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.86 |
Junction analysis
| Reads at junctions: | 15,923,729 |
| ACCT | 5.27% |
| AGGT | 4.82% |
| ATCT | 3.8% |
| AGGA | 3.63% |
| TCCT | 3.46% |
| GCCT | 2.9% |
| AGCT | 2.85% |
| AGGC | 2.38% |
| CCCT | 2.38% |
| AGAT | 2.33% |
| TTCT | 2.22% |
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