Input data and parameters
Input
| Analysis date: | Sun Oct 29 13:01:28 GMT 2023 |
| BAM file: | SRX7354192.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): | 40,015,316 / 39,966,036 |
| Number of aligned pairs (without duplicates): | 39,960,365 |
| Total number of alignments: | 84,729,036 |
| Number of secondary alignments: | 4,747,684 |
| Number of non-unique alignments: | 7,949,656 |
| Aligned to genes: | 65,714,212 |
| Ambiguous alignments: | 205,206 |
| No feature assigned: | 10,595,464 |
| Missing chromosome in annotation: | 264,498 |
| Not aligned: | 9,884,664 |
Reads genomic origin
| Exonic: | 65,714,212 / 86.12% |
| Intronic: | 6,650,094 / 8.71% |
| Intergenic: | 3,945,370 / 5.17% |
| Intronic/intergenic overlapping exon: | 2,798,897 / 3.67% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 21,151,392 |
| ACCT | 5.6% |
| AGGT | 4.65% |
| AGGA | 3.51% |
| ATCT | 3.5% |
| GCCT | 3.29% |
| TCCT | 3.26% |
| AGCT | 2.8% |
| CCCT | 2.47% |
| AGAT | 2.41% |
| AGGC | 2.36% |
| TTCT | 2.19% |

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