Input data and parameters
Input
| Analysis date: | Tue Oct 31 08:37:01 GMT 2023 |
| BAM file: | SRX7354310.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): | 39,417,796 / 39,376,986 |
| Number of aligned pairs (without duplicates): | 39,369,619 |
| Total number of alignments: | 83,246,694 |
| Number of secondary alignments: | 4,451,912 |
| Number of non-unique alignments: | 7,527,701 |
| Aligned to genes: | 66,931,792 |
| Ambiguous alignments: | 247,433 |
| No feature assigned: | 8,324,170 |
| Missing chromosome in annotation: | 215,598 |
| Not aligned: | 10,898,286 |
Reads genomic origin
| Exonic: | 66,931,792 / 88.94% |
| Intronic: | 5,454,985 / 7.25% |
| Intergenic: | 2,869,185 / 3.81% |
| Intronic/intergenic overlapping exon: | 2,771,791 / 3.68% |
Transcript coverage profile
| 5' bias: | 0.25 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 22,152,414 |
| ACCT | 5.73% |
| AGGT | 4.67% |
| ATCT | 3.79% |
| TCCT | 3.61% |
| AGGA | 3.3% |
| GCCT | 3.28% |
| AGCT | 2.55% |
| AGGC | 2.44% |
| CCCT | 2.32% |
| TTCT | 2.05% |
| AGAT | 2.03% |
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