Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:18:06 GMT 2023 |
| BAM file: | SRX7354081.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): | 38,997,959 / 38,958,479 |
| Number of aligned pairs (without duplicates): | 38,937,246 |
| Total number of alignments: | 87,057,297 |
| Number of secondary alignments: | 9,100,859 |
| Number of non-unique alignments: | 11,797,118 |
| Aligned to genes: | 66,015,687 |
| Ambiguous alignments: | 275,444 |
| No feature assigned: | 6,722,402 |
| Missing chromosome in annotation: | 2,246,646 |
| Not aligned: | 6,578,160 |
Reads genomic origin
| Exonic: | 66,015,687 / 90.76% |
| Intronic: | 3,549,566 / 4.88% |
| Intergenic: | 3,172,836 / 4.36% |
| Intronic/intergenic overlapping exon: | 3,329,916 / 4.58% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 2.41 |
Junction analysis
| Reads at junctions: | 20,382,730 |
| ACCT | 5.47% |
| TCCT | 4.87% |
| AGGT | 4.4% |
| ATCT | 4.37% |
| CCCT | 3.91% |
| AGGA | 2.79% |
| AGGC | 2.33% |
| AGAC | 2.27% |
| GCCT | 2.19% |
| AGCT | 2.01% |
| GTCT | 1.96% |
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