Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:28:02 GMT 2023 |
| BAM file: | SRX7354326.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): | 29,093,064 / 29,065,975 |
| Number of aligned pairs (without duplicates): | 29,059,926 |
| Total number of alignments: | 61,777,241 |
| Number of secondary alignments: | 3,618,202 |
| Number of non-unique alignments: | 6,036,853 |
| Aligned to genes: | 50,491,752 |
| Ambiguous alignments: | 176,781 |
| No feature assigned: | 4,842,072 |
| Missing chromosome in annotation: | 229,783 |
| Not aligned: | 3,994,057 |
Reads genomic origin
| Exonic: | 50,491,752 / 91.25% |
| Intronic: | 2,819,118 / 5.09% |
| Intergenic: | 2,022,954 / 3.66% |
| Intronic/intergenic overlapping exon: | 1,790,650 / 3.24% |
Transcript coverage profile
| 5' bias: | 0.18 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.99 |
Junction analysis
| Reads at junctions: | 14,935,348 |
| ACCT | 5.44% |
| AGGT | 4.69% |
| ATCT | 4.51% |
| TCCT | 3.98% |
| GCCT | 3.17% |
| AGGA | 3.14% |
| CCCT | 3.01% |
| TTCT | 2.28% |
| AGGC | 2.21% |
| AGCT | 2.16% |
| AGAA | 1.99% |
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