Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:41:15 GMT 2023 |
| BAM file: | SRX7354227.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): | 44,364,195 / 44,321,425 |
| Number of aligned pairs (without duplicates): | 44,293,687 |
| Total number of alignments: | 94,419,504 |
| Number of secondary alignments: | 5,733,884 |
| Number of non-unique alignments: | 9,332,957 |
| Aligned to genes: | 74,640,944 |
| Ambiguous alignments: | 238,138 |
| No feature assigned: | 9,787,525 |
| Missing chromosome in annotation: | 419,940 |
| Not aligned: | 1,856,844 |
Reads genomic origin
| Exonic: | 74,640,944 / 88.41% |
| Intronic: | 7,425,120 / 8.79% |
| Intergenic: | 2,362,405 / 2.8% |
| Intronic/intergenic overlapping exon: | 3,699,958 / 4.38% |
Transcript coverage profile
| 5' bias: | 0.51 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.97 |
Junction analysis
| Reads at junctions: | 30,034,015 |
| AGGT | 4.91% |
| ACCT | 4.68% |
| ATCT | 4.02% |
| TCCT | 3.76% |
| AGGA | 3.69% |
| AGCT | 3.23% |
| GCCT | 2.72% |
| CCCT | 2.44% |
| AGGC | 2.4% |
| AGAT | 2.03% |
| AGGG | 1.99% |
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