Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:58:18 GMT 2023 |
| BAM file: | SRX7354116.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): | 62,220,897 / 62,153,948 |
| Number of aligned pairs (without duplicates): | 62,128,381 |
| Total number of alignments: | 132,928,405 |
| Number of secondary alignments: | 8,553,560 |
| Number of non-unique alignments: | 14,003,856 |
| Aligned to genes: | 102,131,318 |
| Ambiguous alignments: | 380,936 |
| No feature assigned: | 15,642,160 |
| Missing chromosome in annotation: | 770,135 |
| Not aligned: | 2,091,043 |
Reads genomic origin
| Exonic: | 102,131,318 / 86.72% |
| Intronic: | 11,342,494 / 9.63% |
| Intergenic: | 4,299,666 / 3.65% |
| Intronic/intergenic overlapping exon: | 5,197,728 / 4.41% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.86 |
Junction analysis
| Reads at junctions: | 37,027,422 |
| ACCT | 5.33% |
| AGGT | 4.74% |
| ATCT | 3.65% |
| AGGA | 3.54% |
| TCCT | 3.48% |
| GCCT | 3.34% |
| AGCT | 2.64% |
| CCCT | 2.62% |
| AGGC | 2.39% |
| AGAT | 2.26% |
| TTCT | 2.12% |
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