Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:02:27 GMT 2023 |
| BAM file: | SRX7354385.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): | 38,480,750 / 38,450,168 |
| Number of aligned pairs (without duplicates): | 38,446,171 |
| Total number of alignments: | 81,522,038 |
| Number of secondary alignments: | 4,591,120 |
| Number of non-unique alignments: | 7,599,712 |
| Aligned to genes: | 59,675,996 |
| Ambiguous alignments: | 215,332 |
| No feature assigned: | 13,690,094 |
| Missing chromosome in annotation: | 340,904 |
| Not aligned: | 4,978,660 |
Reads genomic origin
| Exonic: | 59,675,996 / 81.34% |
| Intronic: | 8,587,705 / 11.71% |
| Intergenic: | 5,102,389 / 6.95% |
| Intronic/intergenic overlapping exon: | 2,866,811 / 3.91% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.26 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 22,117,654 |
| ACCT | 5.19% |
| AGGT | 4.7% |
| AGGA | 3.48% |
| ATCT | 3.46% |
| TCCT | 3.42% |
| GCCT | 3.31% |
| AGCT | 2.77% |
| CCCT | 2.53% |
| AGGC | 2.41% |
| AGAT | 2.27% |
| TTCT | 2.17% |
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