Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:55:51 GMT 2023 |
| BAM file: | SRX7354150.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): | 40,803,528 / 40,757,692 |
| Number of aligned pairs (without duplicates): | 40,701,477 |
| Total number of alignments: | 89,415,847 |
| Number of secondary alignments: | 7,854,627 |
| Number of non-unique alignments: | 10,636,133 |
| Aligned to genes: | 68,665,649 |
| Ambiguous alignments: | 287,450 |
| No feature assigned: | 8,095,545 |
| Missing chromosome in annotation: | 1,731,070 |
| Not aligned: | 4,250,922 |
Reads genomic origin
| Exonic: | 68,665,649 / 89.45% |
| Intronic: | 4,273,332 / 5.57% |
| Intergenic: | 3,822,213 / 4.98% |
| Intronic/intergenic overlapping exon: | 3,365,273 / 4.38% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 21,279,171 |
| ACCT | 5.39% |
| TCCT | 4.49% |
| AGGT | 4.41% |
| ATCT | 4.38% |
| GCCT | 3.53% |
| AGGA | 2.98% |
| CCCT | 2.91% |
| TTCT | 2.3% |
| AGCT | 2.23% |
| AGGC | 2.23% |
| TCCC | 1.75% |
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