Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:52:43 GMT 2023 |
| BAM file: | SRX7354179.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): | 36,770,141 / 36,731,997 |
| Number of aligned pairs (without duplicates): | 36,725,848 |
| Total number of alignments: | 78,096,453 |
| Number of secondary alignments: | 4,594,315 |
| Number of non-unique alignments: | 7,595,099 |
| Aligned to genes: | 61,051,104 |
| Ambiguous alignments: | 242,409 |
| No feature assigned: | 8,932,455 |
| Missing chromosome in annotation: | 275,386 |
| Not aligned: | 9,214,754 |
Reads genomic origin
| Exonic: | 61,051,104 / 87.24% |
| Intronic: | 6,554,731 / 9.37% |
| Intergenic: | 2,377,724 / 3.4% |
| Intronic/intergenic overlapping exon: | 2,479,666 / 3.54% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2.07 |
Junction analysis
| Reads at junctions: | 23,169,242 |
| ACCT | 5.35% |
| AGGT | 4.84% |
| AGGA | 3.6% |
| ATCT | 3.59% |
| TCCT | 3.41% |
| GCCT | 2.92% |
| AGCT | 2.73% |
| CCCT | 2.46% |
| AGGC | 2.45% |
| AGAT | 2.26% |
| TTCT | 2.16% |
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