Input data and parameters
Input
| Analysis date: | Sun Oct 29 13:07:22 GMT 2023 |
| BAM file: | SRX7354151.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): | 39,209,076 / 39,176,786 |
| Number of aligned pairs (without duplicates): | 39,170,967 |
| Total number of alignments: | 82,782,493 |
| Number of secondary alignments: | 4,396,631 |
| Number of non-unique alignments: | 7,375,215 |
| Aligned to genes: | 64,308,824 |
| Ambiguous alignments: | 220,081 |
| No feature assigned: | 10,587,762 |
| Missing chromosome in annotation: | 290,611 |
| Not aligned: | 7,731,602 |
Reads genomic origin
| Exonic: | 64,308,824 / 85.86% |
| Intronic: | 7,313,756 / 9.77% |
| Intergenic: | 3,274,006 / 4.37% |
| Intronic/intergenic overlapping exon: | 2,881,661 / 3.85% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 21,977,265 |
| ACCT | 5.26% |
| AGGT | 4.65% |
| ATCT | 3.73% |
| AGGA | 3.55% |
| TCCT | 3.36% |
| GCCT | 3.12% |
| AGCT | 2.78% |
| AGGC | 2.41% |
| AGAT | 2.33% |
| CCCT | 2.33% |
| TTCT | 2.16% |

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