Input data and parameters
Input
| Analysis date: | Tue Oct 31 17:22:57 GMT 2023 |
| BAM file: | SRX7354399.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): | 34,397,778 / 34,367,993 |
| Number of aligned pairs (without duplicates): | 34,364,255 |
| Total number of alignments: | 73,559,242 |
| Number of secondary alignments: | 4,793,471 |
| Number of non-unique alignments: | 7,789,852 |
| Aligned to genes: | 56,554,545 |
| Ambiguous alignments: | 201,027 |
| No feature assigned: | 8,622,371 |
| Missing chromosome in annotation: | 391,447 |
| Not aligned: | 3,216,021 |
Reads genomic origin
| Exonic: | 56,554,545 / 86.77% |
| Intronic: | 5,942,717 / 9.12% |
| Intergenic: | 2,679,654 / 4.11% |
| Intronic/intergenic overlapping exon: | 2,017,978 / 3.1% |
Transcript coverage profile
| 5' bias: | 0.44 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 18,641,697 |
| ACCT | 5.3% |
| AGGT | 4.65% |
| ATCT | 3.57% |
| AGGA | 3.51% |
| TCCT | 3.4% |
| GCCT | 3.14% |
| AGCT | 2.76% |
| TTCT | 2.59% |
| CCCT | 2.38% |
| AGGC | 2.31% |
| AGAT | 2.25% |
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