Input data and parameters
Input
| Analysis date: | Mon Oct 30 13:01:20 GMT 2023 |
| BAM file: | SRX7354197.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): | 43,685,919 / 43,663,152 |
| Number of aligned pairs (without duplicates): | 43,655,439 |
| Total number of alignments: | 94,007,562 |
| Number of secondary alignments: | 6,658,491 |
| Number of non-unique alignments: | 10,516,551 |
| Aligned to genes: | 74,543,795 |
| Ambiguous alignments: | 287,933 |
| No feature assigned: | 7,993,083 |
| Missing chromosome in annotation: | 666,200 |
| Not aligned: | 1,796,643 |
Reads genomic origin
| Exonic: | 74,543,795 / 90.32% |
| Intronic: | 5,294,511 / 6.41% |
| Intergenic: | 2,698,572 / 3.27% |
| Intronic/intergenic overlapping exon: | 3,211,938 / 3.89% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 2.04 |
Junction analysis
| Reads at junctions: | 25,747,278 |
| ACCT | 5.32% |
| AGGT | 4.54% |
| TCCT | 4.2% |
| ATCT | 4.18% |
| AGGA | 3.18% |
| GCCT | 3.03% |
| CCCT | 2.63% |
| AGCT | 2.44% |
| AGGC | 2.33% |
| TTCT | 2.08% |
| AGAA | 1.83% |
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