Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:26:57 GMT 2023 |
| BAM file: | SRX7354158.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): | 38,040,597 / 38,020,033 |
| Number of aligned pairs (without duplicates): | 38,017,133 |
| Total number of alignments: | 80,835,963 |
| Number of secondary alignments: | 4,775,333 |
| Number of non-unique alignments: | 8,054,755 |
| Aligned to genes: | 63,604,908 |
| Ambiguous alignments: | 213,872 |
| No feature assigned: | 8,703,730 |
| Missing chromosome in annotation: | 258,698 |
| Not aligned: | 3,390,404 |
Reads genomic origin
| Exonic: | 63,604,908 / 87.96% |
| Intronic: | 6,062,516 / 8.38% |
| Intergenic: | 2,641,214 / 3.65% |
| Intronic/intergenic overlapping exon: | 2,260,038 / 3.13% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.97 |
Junction analysis
| Reads at junctions: | 21,012,666 |
| ACCT | 5.62% |
| AGGT | 4.67% |
| ATCT | 3.63% |
| AGGA | 3.55% |
| TCCT | 3.42% |
| GCCT | 3.39% |
| AGCT | 2.74% |
| AGGC | 2.38% |
| CCCT | 2.36% |
| AGAT | 2.29% |
| TTCT | 2.16% |
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