Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:28:59 GMT 2023 |
| BAM file: | SRX7354232.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): | 40,554,348 / 40,507,349 |
| Number of aligned pairs (without duplicates): | 40,499,637 |
| Total number of alignments: | 85,777,893 |
| Number of secondary alignments: | 4,716,196 |
| Number of non-unique alignments: | 7,866,944 |
| Aligned to genes: | 69,075,639 |
| Ambiguous alignments: | 261,942 |
| No feature assigned: | 8,254,420 |
| Missing chromosome in annotation: | 318,948 |
| Not aligned: | 6,272,243 |
Reads genomic origin
| Exonic: | 69,075,639 / 89.33% |
| Intronic: | 4,862,558 / 6.29% |
| Intergenic: | 3,391,862 / 4.39% |
| Intronic/intergenic overlapping exon: | 2,897,339 / 3.75% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 22,012,731 |
| ACCT | 5.52% |
| AGGT | 4.71% |
| ATCT | 3.89% |
| TCCT | 3.66% |
| GCCT | 3.44% |
| AGGA | 3.4% |
| CCCT | 2.55% |
| AGCT | 2.49% |
| AGGC | 2.4% |
| TTCT | 2.27% |
| AGAT | 2.1% |

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