Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:43:01 GMT 2023 |
| BAM file: | SRX7354059.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): | 32,044,222 / 32,024,451 |
| Number of aligned pairs (without duplicates): | 32,020,437 |
| Total number of alignments: | 68,564,599 |
| Number of secondary alignments: | 4,495,926 |
| Number of non-unique alignments: | 6,961,804 |
| Aligned to genes: | 48,844,279 |
| Ambiguous alignments: | 202,013 |
| No feature assigned: | 12,065,261 |
| Missing chromosome in annotation: | 491,242 |
| Not aligned: | 1,752,511 |
Reads genomic origin
| Exonic: | 48,844,279 / 80.19% |
| Intronic: | 10,083,901 / 16.56% |
| Intergenic: | 1,981,360 / 3.25% |
| Intronic/intergenic overlapping exon: | 2,411,238 / 3.96% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 18,129,667 |
| ACCT | 5.34% |
| AGGT | 4.59% |
| ATCT | 3.62% |
| TCCT | 3.56% |
| AGGA | 3.48% |
| GCCT | 3.06% |
| AGCT | 2.77% |
| AGGC | 2.46% |
| CCCT | 2.42% |
| AGAT | 2.24% |
| TTCT | 2.13% |

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