Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:36:23 GMT 2023 |
| BAM file: | SRX7354095.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): | 31,744,963 / 31,719,529 |
| Number of aligned pairs (without duplicates): | 31,716,232 |
| Total number of alignments: | 67,734,611 |
| Number of secondary alignments: | 4,270,119 |
| Number of non-unique alignments: | 7,274,880 |
| Aligned to genes: | 52,251,375 |
| Ambiguous alignments: | 195,967 |
| No feature assigned: | 7,764,798 |
| Missing chromosome in annotation: | 247,591 |
| Not aligned: | 5,742,492 |
Reads genomic origin
| Exonic: | 52,251,375 / 87.06% |
| Intronic: | 4,626,728 / 7.71% |
| Intergenic: | 3,138,070 / 5.23% |
| Intronic/intergenic overlapping exon: | 2,006,490 / 3.34% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 16,313,785 |
| ACCT | 5.44% |
| AGGT | 4.68% |
| ATCT | 3.61% |
| TCCT | 3.49% |
| AGGA | 3.46% |
| GCCT | 3.35% |
| AGCT | 2.72% |
| CCCT | 2.66% |
| AGGC | 2.41% |
| AGAT | 2.21% |
| TTCT | 2.14% |
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