Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:40:48 GMT 2023 |
| BAM file: | SRX7354290.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): | 68,050,532 / 67,902,973 |
| Number of aligned pairs (without duplicates): | 67,877,470 |
| Total number of alignments: | 144,850,083 |
| Number of secondary alignments: | 8,896,578 |
| Number of non-unique alignments: | 14,898,420 |
| Aligned to genes: | 109,555,403 |
| Ambiguous alignments: | 386,893 |
| No feature assigned: | 19,479,841 |
| Missing chromosome in annotation: | 529,526 |
| Not aligned: | 11,679,931 |
Reads genomic origin
| Exonic: | 109,555,403 / 84.9% |
| Intronic: | 14,091,275 / 10.92% |
| Intergenic: | 5,388,566 / 4.18% |
| Intronic/intergenic overlapping exon: | 5,575,202 / 4.32% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.72 |
Junction analysis
| Reads at junctions: | 36,333,533 |
| ACCT | 5.44% |
| AGGT | 4.71% |
| AGGA | 3.66% |
| ATCT | 3.6% |
| TCCT | 3.31% |
| GCCT | 3.08% |
| AGCT | 2.66% |
| AGAT | 2.5% |
| CCCT | 2.37% |
| AGGC | 2.36% |
| TTCT | 2.18% |
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