Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:59:54 GMT 2023 |
| BAM file: | SRX7354200.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): | 70,763,736 / 70,727,345 |
| Number of aligned pairs (without duplicates): | 70,717,475 |
| Total number of alignments: | 159,175,093 |
| Number of secondary alignments: | 17,684,012 |
| Number of non-unique alignments: | 24,785,780 |
| Aligned to genes: | 118,555,157 |
| Ambiguous alignments: | 477,697 |
| No feature assigned: | 11,663,749 |
| Missing chromosome in annotation: | 3,692,710 |
| Not aligned: | 4,230,557 |
Reads genomic origin
| Exonic: | 118,555,157 / 91.04% |
| Intronic: | 5,711,363 / 4.39% |
| Intergenic: | 5,952,386 / 4.57% |
| Intronic/intergenic overlapping exon: | 6,272,873 / 4.82% |
Transcript coverage profile
| 5' bias: | 0.19 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.08 |
Junction analysis
| Reads at junctions: | 37,769,335 |
| ACCT | 4.89% |
| AGGT | 4.76% |
| ATCT | 4.62% |
| TCCT | 4.04% |
| CCCT | 3.12% |
| AGGA | 3.07% |
| GCCT | 2.65% |
| AGGC | 2.48% |
| AGCT | 2.22% |
| TTCT | 2.06% |
| AGAA | 2.03% |
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