Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:23:26 GMT 2023 |
| BAM file: | SRX7354364.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): | 34,740,486 / 34,720,478 |
| Number of aligned pairs (without duplicates): | 34,701,275 |
| Total number of alignments: | 75,087,935 |
| Number of secondary alignments: | 5,626,971 |
| Number of non-unique alignments: | 9,207,791 |
| Aligned to genes: | 58,857,877 |
| Ambiguous alignments: | 257,335 |
| No feature assigned: | 6,244,729 |
| Missing chromosome in annotation: | 520,203 |
| Not aligned: | 1,446,782 |
Reads genomic origin
| Exonic: | 58,857,877 / 90.41% |
| Intronic: | 3,616,236 / 5.55% |
| Intergenic: | 2,628,493 / 4.04% |
| Intronic/intergenic overlapping exon: | 2,732,252 / 4.2% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.26 |
| 5'-3' bias: | 1.95 |
Junction analysis
| Reads at junctions: | 18,475,952 |
| ACCT | 5.14% |
| TCCT | 4.6% |
| AGGT | 4.44% |
| ATCT | 4.27% |
| CCCT | 3.27% |
| AGGA | 3.19% |
| GCCT | 3.17% |
| AGCT | 2.4% |
| AGGC | 2.27% |
| TTCT | 2.11% |
| GTCT | 1.76% |
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