Input data and parameters
Input
| Analysis date: | Tue Oct 31 16:41:49 GMT 2023 |
| BAM file: | SRX7354393.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): | 126,093,945 / 125,926,247 |
| Number of aligned pairs (without duplicates): | 125,914,605 |
| Total number of alignments: | 270,928,955 |
| Number of secondary alignments: | 18,908,763 |
| Number of non-unique alignments: | 30,390,501 |
| Aligned to genes: | 215,128,352 |
| Ambiguous alignments: | 967,544 |
| No feature assigned: | 22,773,118 |
| Missing chromosome in annotation: | 1,669,440 |
| Not aligned: | 11,107,986 |
Reads genomic origin
| Exonic: | 215,128,352 / 90.43% |
| Intronic: | 15,319,157 / 6.44% |
| Intergenic: | 7,453,961 / 3.13% |
| Intronic/intergenic overlapping exon: | 8,993,078 / 3.78% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.71 |
Junction analysis
| Reads at junctions: | 78,567,120 |
| ACCT | 5.38% |
| AGGT | 4.39% |
| ATCT | 4.1% |
| TCCT | 3.98% |
| GCCT | 3.51% |
| AGGA | 3.12% |
| CCCT | 2.75% |
| TTCT | 2.51% |
| AGCT | 2.48% |
| AGGC | 2.29% |
| AGAT | 1.9% |
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