Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:46:24 GMT 2023 |
| BAM file: | SRX7354355.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): | 37,924,481 / 37,900,771 |
| Number of aligned pairs (without duplicates): | 37,897,593 |
| Total number of alignments: | 80,698,360 |
| Number of secondary alignments: | 4,873,108 |
| Number of non-unique alignments: | 8,289,965 |
| Aligned to genes: | 62,889,147 |
| Ambiguous alignments: | 211,817 |
| No feature assigned: | 9,044,281 |
| Missing chromosome in annotation: | 263,150 |
| Not aligned: | 3,767,248 |
Reads genomic origin
| Exonic: | 62,889,147 / 87.43% |
| Intronic: | 5,704,834 / 7.93% |
| Intergenic: | 3,339,447 / 4.64% |
| Intronic/intergenic overlapping exon: | 2,402,038 / 3.34% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 19,111,827 |
| ACCT | 5.24% |
| AGGT | 4.74% |
| ATCT | 3.74% |
| AGGA | 3.63% |
| TCCT | 3.38% |
| GCCT | 3.17% |
| AGCT | 2.66% |
| CCCT | 2.44% |
| AGGC | 2.37% |
| AGAT | 2.31% |
| TTCT | 2.27% |
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