Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:54:33 GMT 2023 |
| BAM file: | SRX7354356.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): | 35,152,075 / 35,130,677 |
| Number of aligned pairs (without duplicates): | 35,127,068 |
| Total number of alignments: | 74,951,306 |
| Number of secondary alignments: | 4,668,554 |
| Number of non-unique alignments: | 7,834,381 |
| Aligned to genes: | 58,824,585 |
| Ambiguous alignments: | 202,820 |
| No feature assigned: | 7,820,388 |
| Missing chromosome in annotation: | 269,132 |
| Not aligned: | 4,177,960 |
Reads genomic origin
| Exonic: | 58,824,585 / 88.27% |
| Intronic: | 5,233,329 / 7.85% |
| Intergenic: | 2,587,059 / 3.88% |
| Intronic/intergenic overlapping exon: | 2,129,191 / 3.19% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.42 |
Junction analysis
| Reads at junctions: | 17,972,173 |
| ACCT | 5.33% |
| AGGT | 4.7% |
| ATCT | 3.62% |
| AGGA | 3.6% |
| TCCT | 3.51% |
| GCCT | 3.07% |
| AGCT | 2.65% |
| AGGC | 2.34% |
| CCCT | 2.28% |
| AGAT | 2.27% |
| TTCT | 2.11% |
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