Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:34:04 GMT 2023 |
| BAM file: | SRX7354130.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): | 31,335,323 / 31,316,968 |
| Number of aligned pairs (without duplicates): | 31,314,576 |
| Total number of alignments: | 67,496,646 |
| Number of secondary alignments: | 4,844,355 |
| Number of non-unique alignments: | 7,645,990 |
| Aligned to genes: | 50,352,379 |
| Ambiguous alignments: | 166,880 |
| No feature assigned: | 8,825,825 |
| Missing chromosome in annotation: | 505,572 |
| Not aligned: | 1,353,825 |
Reads genomic origin
| Exonic: | 50,352,379 / 85.09% |
| Intronic: | 6,488,200 / 10.96% |
| Intergenic: | 2,337,625 / 3.95% |
| Intronic/intergenic overlapping exon: | 1,978,654 / 3.34% |
Transcript coverage profile
| 5' bias: | 0.46 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 15,526,091 |
| ACCT | 5.14% |
| AGGT | 4.59% |
| ATCT | 3.68% |
| AGGA | 3.49% |
| TCCT | 3.41% |
| GCCT | 2.96% |
| AGCT | 2.88% |
| CCCT | 2.47% |
| AGGC | 2.34% |
| TTCT | 2.23% |
| AGAT | 2.22% |
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