Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:23:41 GMT 2023 |
| BAM file: | SRX7354056.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): | 34,899,189 / 34,876,402 |
| Number of aligned pairs (without duplicates): | 34,873,718 |
| Total number of alignments: | 74,435,635 |
| Number of secondary alignments: | 4,660,044 |
| Number of non-unique alignments: | 7,611,070 |
| Aligned to genes: | 58,528,694 |
| Ambiguous alignments: | 212,822 |
| No feature assigned: | 7,717,364 |
| Missing chromosome in annotation: | 365,685 |
| Not aligned: | 2,114,851 |
Reads genomic origin
| Exonic: | 58,528,694 / 88.35% |
| Intronic: | 5,518,300 / 8.33% |
| Intergenic: | 2,199,064 / 3.32% |
| Intronic/intergenic overlapping exon: | 2,266,523 / 3.42% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.81 |
Junction analysis
| Reads at junctions: | 20,776,077 |
| ACCT | 5.35% |
| AGGT | 4.53% |
| ATCT | 3.77% |
| TCCT | 3.6% |
| AGGA | 3.35% |
| GCCT | 3.34% |
| AGCT | 2.68% |
| CCCT | 2.42% |
| AGGC | 2.36% |
| TTCT | 2.15% |
| AGAT | 2.09% |

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