Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:55:17 GMT 2023 |
| BAM file: | SRX7354411.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): | 36,469,457 / 36,447,898 |
| Number of aligned pairs (without duplicates): | 36,443,652 |
| Total number of alignments: | 77,026,752 |
| Number of secondary alignments: | 4,109,397 |
| Number of non-unique alignments: | 6,722,927 |
| Aligned to genes: | 60,459,420 |
| Ambiguous alignments: | 215,088 |
| No feature assigned: | 9,307,519 |
| Missing chromosome in annotation: | 321,798 |
| Not aligned: | 3,068,627 |
Reads genomic origin
| Exonic: | 60,459,420 / 86.66% |
| Intronic: | 6,604,193 / 9.47% |
| Intergenic: | 2,703,326 / 3.87% |
| Intronic/intergenic overlapping exon: | 2,522,699 / 3.62% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.71 |
Junction analysis
| Reads at junctions: | 19,423,659 |
| ACCT | 5.35% |
| AGGT | 4.66% |
| ATCT | 3.6% |
| AGGA | 3.58% |
| TCCT | 3.38% |
| GCCT | 3.22% |
| AGCT | 2.76% |
| CCCT | 2.37% |
| AGGC | 2.32% |
| AGAT | 2.26% |
| TTCT | 2.05% |
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