Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:36:52 GMT 2023 |
| BAM file: | SRX7354293.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): | 29,193,752 / 29,176,535 |
| Number of aligned pairs (without duplicates): | 29,172,597 |
| Total number of alignments: | 61,630,413 |
| Number of secondary alignments: | 3,260,126 |
| Number of non-unique alignments: | 5,400,306 |
| Aligned to genes: | 48,729,914 |
| Ambiguous alignments: | 147,920 |
| No feature assigned: | 7,122,336 |
| Missing chromosome in annotation: | 229,937 |
| Not aligned: | 3,859,059 |
Reads genomic origin
| Exonic: | 48,729,914 / 87.25% |
| Intronic: | 4,849,464 / 8.68% |
| Intergenic: | 2,272,872 / 4.07% |
| Intronic/intergenic overlapping exon: | 1,719,920 / 3.08% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.36 |
Junction analysis
| Reads at junctions: | 14,955,335 |
| ACCT | 5.41% |
| AGGT | 4.74% |
| ATCT | 3.83% |
| AGGA | 3.65% |
| TCCT | 3.63% |
| GCCT | 3.02% |
| AGCT | 2.63% |
| AGGC | 2.36% |
| CCCT | 2.34% |
| AGAT | 2.26% |
| TTCT | 2.21% |
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