Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:16:44 GMT 2023 |
| BAM file: | SRX7354178.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): | 46,933,012 / 46,877,524 |
| Number of aligned pairs (without duplicates): | 46,861,052 |
| Total number of alignments: | 103,700,501 |
| Number of secondary alignments: | 9,889,965 |
| Number of non-unique alignments: | 12,245,016 |
| Aligned to genes: | 75,869,105 |
| Ambiguous alignments: | 287,596 |
| No feature assigned: | 12,590,690 |
| Missing chromosome in annotation: | 2,708,094 |
| Not aligned: | 2,147,306 |
Reads genomic origin
| Exonic: | 75,869,105 / 85.77% |
| Intronic: | 9,696,728 / 10.96% |
| Intergenic: | 2,893,962 / 3.27% |
| Intronic/intergenic overlapping exon: | 3,763,576 / 4.25% |
Transcript coverage profile
| 5' bias: | 0.49 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 28,165,505 |
| ACCT | 5.27% |
| AGGT | 4.7% |
| ATCT | 3.65% |
| TCCT | 3.44% |
| AGGA | 3.4% |
| GCCT | 3.32% |
| AGCT | 2.77% |
| CCCT | 2.63% |
| AGGC | 2.42% |
| AGAT | 2.13% |
| TTCT | 2.1% |
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