Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:18:57 GMT 2023 |
| BAM file: | SRX7354049.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): | 44,037,452 / 44,003,256 |
| Number of aligned pairs (without duplicates): | 43,997,586 |
| Total number of alignments: | 93,616,528 |
| Number of secondary alignments: | 5,575,820 |
| Number of non-unique alignments: | 9,305,861 |
| Aligned to genes: | 70,431,424 |
| Ambiguous alignments: | 246,340 |
| No feature assigned: | 13,279,447 |
| Missing chromosome in annotation: | 353,456 |
| Not aligned: | 4,901,880 |
Reads genomic origin
| Exonic: | 70,431,424 / 84.14% |
| Intronic: | 10,164,642 / 12.14% |
| Intergenic: | 3,114,805 / 3.72% |
| Intronic/intergenic overlapping exon: | 2,983,825 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.31 |
Junction analysis
| Reads at junctions: | 22,475,219 |
| ACCT | 5.2% |
| AGGT | 4.82% |
| AGGA | 3.75% |
| ATCT | 3.61% |
| TCCT | 3.54% |
| GCCT | 2.77% |
| AGCT | 2.76% |
| CCCT | 2.4% |
| AGGC | 2.38% |
| AGAT | 2.37% |
| TTCT | 2.2% |
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