Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:19:11 GMT 2023 |
| BAM file: | SRX7354236.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): | 36,441,553 / 36,427,076 |
| Number of aligned pairs (without duplicates): | 36,424,031 |
| Total number of alignments: | 77,365,448 |
| Number of secondary alignments: | 4,496,819 |
| Number of non-unique alignments: | 7,589,668 |
| Aligned to genes: | 61,923,542 |
| Ambiguous alignments: | 222,453 |
| No feature assigned: | 7,369,929 |
| Missing chromosome in annotation: | 259,856 |
| Not aligned: | 2,743,845 |
Reads genomic origin
| Exonic: | 61,923,542 / 89.36% |
| Intronic: | 4,815,420 / 6.95% |
| Intergenic: | 2,554,509 / 3.69% |
| Intronic/intergenic overlapping exon: | 2,098,652 / 3.03% |
Transcript coverage profile
| 5' bias: | 0.29 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.1 |
Junction analysis
| Reads at junctions: | 20,132,021 |
| ACCT | 5.36% |
| AGGT | 4.9% |
| ATCT | 3.79% |
| AGGA | 3.65% |
| TCCT | 3.56% |
| GCCT | 2.95% |
| AGCT | 2.77% |
| CCCT | 2.5% |
| AGGC | 2.38% |
| AGAT | 2.32% |
| TTCT | 2.18% |
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