Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:13:16 GMT 2023 |
| BAM file: | SRX7354062.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): | 35,100,543 / 35,078,030 |
| Number of aligned pairs (without duplicates): | 35,074,928 |
| Total number of alignments: | 74,441,056 |
| Number of secondary alignments: | 4,262,483 |
| Number of non-unique alignments: | 7,147,751 |
| Aligned to genes: | 58,572,335 |
| Ambiguous alignments: | 206,695 |
| No feature assigned: | 8,265,005 |
| Missing chromosome in annotation: | 249,270 |
| Not aligned: | 3,702,861 |
Reads genomic origin
| Exonic: | 58,572,335 / 87.63% |
| Intronic: | 5,749,844 / 8.6% |
| Intergenic: | 2,515,161 / 3.76% |
| Intronic/intergenic overlapping exon: | 2,197,145 / 3.29% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 18,437,877 |
| ACCT | 5.33% |
| AGGT | 4.78% |
| ATCT | 3.64% |
| AGGA | 3.62% |
| TCCT | 3.43% |
| GCCT | 2.86% |
| AGCT | 2.7% |
| TTCT | 2.66% |
| AGAT | 2.39% |
| AGGC | 2.34% |
| CCCT | 2.29% |
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