Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:18:28 GMT 2023 |
| BAM file: | SRX7354248.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): | 43,952,706 / 43,935,119 |
| Number of aligned pairs (without duplicates): | 43,910,265 |
| Total number of alignments: | 95,208,361 |
| Number of secondary alignments: | 7,320,536 |
| Number of non-unique alignments: | 11,875,802 |
| Aligned to genes: | 74,847,809 |
| Ambiguous alignments: | 278,911 |
| No feature assigned: | 7,544,234 |
| Missing chromosome in annotation: | 661,605 |
| Not aligned: | 3,592,109 |
Reads genomic origin
| Exonic: | 74,847,809 / 90.84% |
| Intronic: | 4,301,060 / 5.22% |
| Intergenic: | 3,243,174 / 3.94% |
| Intronic/intergenic overlapping exon: | 3,308,996 / 4.02% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.54 |
Junction analysis
| Reads at junctions: | 24,602,331 |
| ACCT | 4.85% |
| ATCT | 4.82% |
| TCCT | 4.6% |
| AGGT | 4.41% |
| CCCT | 3.5% |
| AGGA | 2.84% |
| AGGC | 2.5% |
| GCCT | 2.26% |
| AGAC | 2.14% |
| TTCT | 2.03% |
| AGCT | 2.01% |

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