Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:36:59 GMT 2023 |
| BAM file: | SRX7354297.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): | 179,477,962 / 179,182,277 |
| Number of aligned pairs (without duplicates): | 179,130,875 |
| Total number of alignments: | 392,664,657 |
| Number of secondary alignments: | 34,004,418 |
| Number of non-unique alignments: | 41,113,842 |
| Aligned to genes: | 272,896,516 |
| Ambiguous alignments: | 1,281,608 |
| No feature assigned: | 68,383,258 |
| Missing chromosome in annotation: | 8,989,433 |
| Not aligned: | 14,198,237 |
Reads genomic origin
| Exonic: | 272,896,516 / 79.96% |
| Intronic: | 60,072,824 / 17.6% |
| Intergenic: | 8,310,434 / 2.44% |
| Intronic/intergenic overlapping exon: | 15,755,018 / 4.62% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 112,639,441 |
| ACCT | 5.11% |
| AGGT | 4.61% |
| ATCT | 3.63% |
| AGGA | 3.61% |
| TCCT | 3.46% |
| GCCT | 3.11% |
| AGCT | 2.74% |
| CCCT | 2.53% |
| AGGC | 2.37% |
| AGAT | 2.29% |
| TTCT | 2.22% |
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