Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:46:09 GMT 2023 |
| BAM file: | SRX7354077.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): | 77,080,409 / 76,937,265 |
| Number of aligned pairs (without duplicates): | 76,926,539 |
| Total number of alignments: | 163,471,885 |
| Number of secondary alignments: | 9,454,211 |
| Number of non-unique alignments: | 14,747,971 |
| Aligned to genes: | 127,773,214 |
| Ambiguous alignments: | 464,162 |
| No feature assigned: | 19,359,488 |
| Missing chromosome in annotation: | 1,127,050 |
| Not aligned: | 12,614,118 |
Reads genomic origin
| Exonic: | 127,773,214 / 86.84% |
| Intronic: | 12,508,592 / 8.5% |
| Intergenic: | 6,850,896 / 4.66% |
| Intronic/intergenic overlapping exon: | 6,118,082 / 4.16% |
Transcript coverage profile
| 5' bias: | 0.49 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 53,602,932 |
| ACCT | 5.15% |
| AGGT | 4.77% |
| TCCT | 3.54% |
| AGGA | 3.44% |
| ATCT | 3.36% |
| GCCT | 3.12% |
| AGCT | 2.81% |
| CCCT | 2.53% |
| AGGC | 2.41% |
| AGAT | 2.18% |
| TTCT | 2.17% |

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