Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:13:54 GMT 2023 |
| BAM file: | SRX7354311.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): | 52,882,898 / 52,839,827 |
| Number of aligned pairs (without duplicates): | 52,830,212 |
| Total number of alignments: | 127,120,041 |
| Number of secondary alignments: | 21,397,316 |
| Number of non-unique alignments: | 21,954,087 |
| Aligned to genes: | 88,066,390 |
| Ambiguous alignments: | 383,625 |
| No feature assigned: | 8,867,694 |
| Missing chromosome in annotation: | 7,848,245 |
| Not aligned: | 3,512,865 |
Reads genomic origin
| Exonic: | 88,066,390 / 90.85% |
| Intronic: | 5,110,156 / 5.27% |
| Intergenic: | 3,757,538 / 3.88% |
| Intronic/intergenic overlapping exon: | 3,661,313 / 3.78% |
Transcript coverage profile
| 5' bias: | 0.14 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.58 |
Junction analysis
| Reads at junctions: | 30,284,187 |
| TCCT | 4.72% |
| AGGT | 4.64% |
| ACCT | 4.63% |
| ATCT | 3.71% |
| AGGA | 3.37% |
| CCCT | 2.73% |
| AGGC | 2.46% |
| AGCT | 2.18% |
| AGAC | 1.93% |
| TTCT | 1.88% |
| GCCT | 1.87% |
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