Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:19:56 GMT 2023 |
| BAM file: | SRX7354088.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): | 38,524,073 / 38,489,984 |
| Number of aligned pairs (without duplicates): | 38,453,304 |
| Total number of alignments: | 90,347,357 |
| Number of secondary alignments: | 13,333,300 |
| Number of non-unique alignments: | 18,998,700 |
| Aligned to genes: | 52,448,124 |
| Ambiguous alignments: | 224,684 |
| No feature assigned: | 16,104,246 |
| Missing chromosome in annotation: | 2,571,603 |
| Not aligned: | 4,378,773 |
Reads genomic origin
| Exonic: | 52,448,124 / 76.51% |
| Intronic: | 7,240,639 / 10.56% |
| Intergenic: | 8,863,607 / 12.93% |
| Intronic/intergenic overlapping exon: | 4,240,578 / 6.19% |
Transcript coverage profile
| 5' bias: | 0.09 |
| 3' bias: | 0.11 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 18,228,230 |
| TCCT | 8.44% |
| ATCT | 6.04% |
| ACCT | 4.78% |
| CCCT | 4.3% |
| AGGT | 3.34% |
| GTCT | 3.28% |
| TCCG | 3.19% |
| AGGA | 2.76% |
| TTCT | 2.42% |
| AGAC | 2.09% |
| GCCT | 1.93% |
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