Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:49:30 GMT 2023 |
| BAM file: | SRX7354160.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): | 37,000,964 / 36,979,190 |
| Number of aligned pairs (without duplicates): | 36,975,951 |
| Total number of alignments: | 79,722,844 |
| Number of secondary alignments: | 5,742,690 |
| Number of non-unique alignments: | 9,644,916 |
| Aligned to genes: | 63,442,726 |
| Ambiguous alignments: | 215,484 |
| No feature assigned: | 5,955,001 |
| Missing chromosome in annotation: | 464,717 |
| Not aligned: | 1,950,284 |
Reads genomic origin
| Exonic: | 63,442,726 / 91.42% |
| Intronic: | 3,350,823 / 4.83% |
| Intergenic: | 2,604,178 / 3.75% |
| Intronic/intergenic overlapping exon: | 2,473,623 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 21,100,754 |
| ACCT | 5.51% |
| AGGT | 4.51% |
| ATCT | 3.54% |
| GCCT | 3.51% |
| TCCT | 3.47% |
| AGGA | 3.35% |
| AGCT | 2.63% |
| AGGC | 2.33% |
| CCCT | 2.29% |
| TTCT | 2.11% |
| AGAT | 2.07% |
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