Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:42:07 GMT 2023 |
| BAM file: | SRX7354057.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): | 37,022,810 / 36,993,632 |
| Number of aligned pairs (without duplicates): | 36,990,630 |
| Total number of alignments: | 79,346,136 |
| Number of secondary alignments: | 5,329,694 |
| Number of non-unique alignments: | 8,852,599 |
| Aligned to genes: | 61,068,937 |
| Ambiguous alignments: | 249,758 |
| No feature assigned: | 8,806,684 |
| Missing chromosome in annotation: | 368,158 |
| Not aligned: | 2,353,108 |
Reads genomic origin
| Exonic: | 61,068,937 / 87.4% |
| Intronic: | 6,477,740 / 9.27% |
| Intergenic: | 2,328,944 / 3.33% |
| Intronic/intergenic overlapping exon: | 2,471,330 / 3.54% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.73 |
Junction analysis
| Reads at junctions: | 22,097,158 |
| ACCT | 5.34% |
| AGGT | 4.61% |
| ATCT | 3.45% |
| TCCT | 3.45% |
| GCCT | 3.44% |
| AGGA | 3.4% |
| AGCT | 2.77% |
| CCCT | 2.47% |
| AGGC | 2.37% |
| AGAT | 2.2% |
| TTCT | 2.19% |
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