Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:37:42 GMT 2023 |
| BAM file: | SRX7354060.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): | 34,098,842 / 34,079,141 |
| Number of aligned pairs (without duplicates): | 34,075,658 |
| Total number of alignments: | 72,510,309 |
| Number of secondary alignments: | 4,332,326 |
| Number of non-unique alignments: | 6,931,902 |
| Aligned to genes: | 54,809,512 |
| Ambiguous alignments: | 188,763 |
| No feature assigned: | 10,190,684 |
| Missing chromosome in annotation: | 389,448 |
| Not aligned: | 2,861,333 |
Reads genomic origin
| Exonic: | 54,809,512 / 84.32% |
| Intronic: | 7,253,630 / 11.16% |
| Intergenic: | 2,937,054 / 4.52% |
| Intronic/intergenic overlapping exon: | 2,187,237 / 3.36% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 17,134,932 |
| ACCT | 5.35% |
| AGGT | 4.74% |
| AGGA | 3.57% |
| ATCT | 3.54% |
| TCCT | 3.45% |
| GCCT | 3.12% |
| AGCT | 2.76% |
| CCCT | 2.38% |
| AGGC | 2.37% |
| AGAT | 2.32% |
| TTCT | 2.16% |

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