Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:24:09 GMT 2023 |
| BAM file: | SRX7354121.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): | 34,238,502 / 34,221,072 |
| Number of aligned pairs (without duplicates): | 34,217,632 |
| Total number of alignments: | 72,718,384 |
| Number of secondary alignments: | 4,258,810 |
| Number of non-unique alignments: | 6,987,413 |
| Aligned to genes: | 57,048,141 |
| Ambiguous alignments: | 216,830 |
| No feature assigned: | 8,155,912 |
| Missing chromosome in annotation: | 310,088 |
| Not aligned: | 3,391,698 |
Reads genomic origin
| Exonic: | 57,048,141 / 87.49% |
| Intronic: | 6,106,600 / 9.37% |
| Intergenic: | 2,049,312 / 3.14% |
| Intronic/intergenic overlapping exon: | 2,120,627 / 3.25% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.8 |
Junction analysis
| Reads at junctions: | 20,814,667 |
| ACCT | 5.47% |
| AGGT | 4.54% |
| AGGA | 3.47% |
| GCCT | 3.47% |
| ATCT | 3.46% |
| TCCT | 3.4% |
| AGCT | 2.78% |
| AGGC | 2.37% |
| CCCT | 2.3% |
| AGAT | 2.28% |
| TTCT | 2.01% |
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