Input data and parameters
Input
| Analysis date: | Tue Oct 31 15:43:35 GMT 2023 |
| BAM file: | SRX7354404.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): | 45,243,192 / 45,182,727 |
| Number of aligned pairs (without duplicates): | 45,145,836 |
| Total number of alignments: | 97,423,567 |
| Number of secondary alignments: | 6,997,648 |
| Number of non-unique alignments: | 11,808,304 |
| Aligned to genes: | 75,937,352 |
| Ambiguous alignments: | 312,660 |
| No feature assigned: | 8,921,364 |
| Missing chromosome in annotation: | 443,887 |
| Not aligned: | 4,794,239 |
Reads genomic origin
| Exonic: | 75,937,352 / 89.49% |
| Intronic: | 5,747,869 / 6.77% |
| Intergenic: | 3,173,495 / 3.74% |
| Intronic/intergenic overlapping exon: | 3,901,100 / 4.6% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 2.03 |
Junction analysis
| Reads at junctions: | 30,011,382 |
| ACCT | 5.43% |
| AGGT | 4.53% |
| ATCT | 4.26% |
| TCCT | 4.06% |
| GCCT | 3.42% |
| AGGA | 3.05% |
| CCCT | 2.86% |
| AGCT | 2.45% |
| AGGC | 2.45% |
| TTCT | 2.31% |
| AGAA | 1.74% |
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