Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:46:35 GMT 2023 |
| BAM file: | SRX7354354.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): | 31,747,210 / 31,725,434 |
| Number of aligned pairs (without duplicates): | 31,720,308 |
| Total number of alignments: | 70,026,674 |
| Number of secondary alignments: | 6,554,030 |
| Number of non-unique alignments: | 8,632,244 |
| Aligned to genes: | 54,497,215 |
| Ambiguous alignments: | 233,717 |
| No feature assigned: | 5,214,594 |
| Missing chromosome in annotation: | 1,448,904 |
| Not aligned: | 3,049,144 |
Reads genomic origin
| Exonic: | 54,497,215 / 91.27% |
| Intronic: | 3,008,902 / 5.04% |
| Intergenic: | 2,205,692 / 3.69% |
| Intronic/intergenic overlapping exon: | 2,105,165 / 3.53% |
Transcript coverage profile
| 5' bias: | 0.18 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 17,886,771 |
| ACCT | 5.23% |
| TCCT | 4.86% |
| ATCT | 4.83% |
| AGGT | 4.25% |
| CCCT | 3.23% |
| AGGA | 3.01% |
| GCCT | 2.88% |
| TTCT | 2.22% |
| AGCT | 2.17% |
| AGGC | 2.13% |
| GTCT | 1.82% |
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