Input data and parameters
Input
| Analysis date: | Sun Oct 29 03:11:15 GMT 2023 |
| BAM file: | SRX7354128.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): | 46,032,500 / 45,962,552 |
| Number of aligned pairs (without duplicates): | 45,956,236 |
| Total number of alignments: | 97,964,144 |
| Number of secondary alignments: | 5,969,092 |
| Number of non-unique alignments: | 10,173,868 |
| Aligned to genes: | 76,203,919 |
| Ambiguous alignments: | 243,861 |
| No feature assigned: | 11,005,406 |
| Missing chromosome in annotation: | 337,090 |
| Not aligned: | 6,763,126 |
Reads genomic origin
| Exonic: | 76,203,919 / 87.38% |
| Intronic: | 6,821,866 / 7.82% |
| Intergenic: | 4,183,540 / 4.8% |
| Intronic/intergenic overlapping exon: | 2,978,549 / 3.42% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.76 |
Junction analysis
| Reads at junctions: | 22,900,508 |
| ACCT | 5.45% |
| AGGT | 4.57% |
| ATCT | 3.59% |
| AGGA | 3.53% |
| TCCT | 3.3% |
| GCCT | 3.28% |
| AGCT | 2.72% |
| CCCT | 2.38% |
| AGGC | 2.34% |
| AGAT | 2.27% |
| TTCT | 2.22% |

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