Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:27:41 GMT 2023 |
| BAM file: | SRX7354271.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): | 41,483,626 / 41,451,093 |
| Number of aligned pairs (without duplicates): | 41,447,561 |
| Total number of alignments: | 87,736,408 |
| Number of secondary alignments: | 4,801,689 |
| Number of non-unique alignments: | 8,092,240 |
| Aligned to genes: | 71,296,545 |
| Ambiguous alignments: | 219,525 |
| No feature assigned: | 7,799,261 |
| Missing chromosome in annotation: | 328,837 |
| Not aligned: | 2,855,393 |
Reads genomic origin
| Exonic: | 71,296,545 / 90.14% |
| Intronic: | 4,462,095 / 5.64% |
| Intergenic: | 3,337,166 / 4.22% |
| Intronic/intergenic overlapping exon: | 2,717,662 / 3.44% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.28 |
Junction analysis
| Reads at junctions: | 23,632,681 |
| ACCT | 5.4% |
| AGGT | 4.67% |
| AGGA | 3.6% |
| ATCT | 3.52% |
| TCCT | 3.4% |
| GCCT | 3.11% |
| AGCT | 2.75% |
| AGGC | 2.38% |
| AGAT | 2.32% |
| CCCT | 2.28% |
| TTCT | 2.12% |
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