Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:03:44 GMT 2023 |
| BAM file: | SRX7354274.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): | 23,569,142 / 23,558,672 |
| Number of aligned pairs (without duplicates): | 23,555,663 |
| Total number of alignments: | 54,185,546 |
| Number of secondary alignments: | 7,057,732 |
| Number of non-unique alignments: | 9,301,734 |
| Aligned to genes: | 33,067,568 |
| Ambiguous alignments: | 160,673 |
| No feature assigned: | 10,048,298 |
| Missing chromosome in annotation: | 1,607,273 |
| Not aligned: | 1,368,460 |
Reads genomic origin
| Exonic: | 33,067,568 / 76.69% |
| Intronic: | 5,031,996 / 11.67% |
| Intergenic: | 5,016,302 / 11.63% |
| Intronic/intergenic overlapping exon: | 1,551,098 / 3.6% |
Transcript coverage profile
| 5' bias: | 0.21 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 2.08 |
Junction analysis
| Reads at junctions: | 14,157,551 |
| ACCT | 4.76% |
| TCCT | 4.62% |
| AGGT | 4.47% |
| ATCT | 3.96% |
| AGGA | 3.08% |
| CCCT | 2.88% |
| GCCT | 2.51% |
| AGGC | 2.31% |
| AGCT | 2.2% |
| TTCT | 2.16% |
| GTCT | 2.11% |
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