Input data and parameters
Input
| Analysis date: | Tue Oct 31 14:11:54 GMT 2023 |
| BAM file: | SRX7354386.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): | 66,895,681 / 66,857,980 |
| Number of aligned pairs (without duplicates): | 66,849,125 |
| Total number of alignments: | 144,113,613 |
| Number of secondary alignments: | 10,359,952 |
| Number of non-unique alignments: | 16,946,433 |
| Aligned to genes: | 113,868,354 |
| Ambiguous alignments: | 515,524 |
| No feature assigned: | 11,959,955 |
| Missing chromosome in annotation: | 823,347 |
| Not aligned: | 3,763,335 |
Reads genomic origin
| Exonic: | 113,868,354 / 90.5% |
| Intronic: | 8,023,914 / 6.38% |
| Intergenic: | 3,936,041 / 3.13% |
| Intronic/intergenic overlapping exon: | 4,952,816 / 3.94% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 39,083,663 |
| ACCT | 5.43% |
| AGGT | 4.39% |
| TCCT | 4.12% |
| ATCT | 4.09% |
| GCCT | 3.58% |
| AGGA | 3.08% |
| CCCT | 2.84% |
| AGCT | 2.3% |
| AGGC | 2.23% |
| TTCT | 2.18% |
| TCCC | 1.78% |
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