Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:25:10 GMT 2023 |
| BAM file: | SRX7354316.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): | 54,714,946 / 54,636,432 |
| Number of aligned pairs (without duplicates): | 54,618,939 |
| Total number of alignments: | 116,346,291 |
| Number of secondary alignments: | 6,994,913 |
| Number of non-unique alignments: | 11,921,690 |
| Aligned to genes: | 87,826,865 |
| Ambiguous alignments: | 272,270 |
| No feature assigned: | 15,967,534 |
| Missing chromosome in annotation: | 357,932 |
| Not aligned: | 7,905,778 |
Reads genomic origin
| Exonic: | 87,826,865 / 84.62% |
| Intronic: | 11,152,896 / 10.75% |
| Intergenic: | 4,814,638 / 4.64% |
| Intronic/intergenic overlapping exon: | 4,273,996 / 4.12% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 25,961,223 |
| ACCT | 5.15% |
| AGGT | 4.7% |
| ATCT | 3.72% |
| AGGA | 3.7% |
| TCCT | 3.27% |
| GCCT | 3.07% |
| AGCT | 2.77% |
| AGAT | 2.48% |
| AGGC | 2.38% |
| CCCT | 2.37% |
| TTCT | 2.25% |
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