Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:41:20 GMT 2023 |
| BAM file: | SRX7354117.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): | 31,478,525 / 31,456,292 |
| Number of aligned pairs (without duplicates): | 31,453,213 |
| Total number of alignments: | 67,093,216 |
| Number of secondary alignments: | 4,158,399 |
| Number of non-unique alignments: | 6,775,395 |
| Aligned to genes: | 53,145,382 |
| Ambiguous alignments: | 181,085 |
| No feature assigned: | 6,589,258 |
| Missing chromosome in annotation: | 402,096 |
| Not aligned: | 1,585,659 |
Reads genomic origin
| Exonic: | 53,145,382 / 88.97% |
| Intronic: | 4,412,444 / 7.39% |
| Intergenic: | 2,176,814 / 3.64% |
| Intronic/intergenic overlapping exon: | 2,071,045 / 3.47% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 18,158,070 |
| ACCT | 5.29% |
| AGGT | 4.54% |
| ATCT | 3.85% |
| GCCT | 3.45% |
| AGGA | 3.38% |
| TCCT | 3.26% |
| AGCT | 2.74% |
| CCCT | 2.62% |
| TTCT | 2.44% |
| AGGC | 2.29% |
| AGAT | 2.04% |
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