Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:52:12 GMT 2023 |
| BAM file: | SRX7354110.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): | 42,220,712 / 42,025,629 |
| Number of aligned pairs (without duplicates): | 41,988,929 |
| Total number of alignments: | 91,067,854 |
| Number of secondary alignments: | 6,821,513 |
| Number of non-unique alignments: | 10,991,058 |
| Aligned to genes: | 59,990,235 |
| Ambiguous alignments: | 187,634 |
| No feature assigned: | 19,249,321 |
| Missing chromosome in annotation: | 649,606 |
| Not aligned: | 18,192,759 |
Reads genomic origin
| Exonic: | 59,990,235 / 75.71% |
| Intronic: | 9,540,020 / 12.04% |
| Intergenic: | 9,709,301 / 12.25% |
| Intronic/intergenic overlapping exon: | 3,525,885 / 4.45% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.27 |
| 5'-3' bias: | 1.69 |
Junction analysis
| Reads at junctions: | 19,307,242 |
| ACCT | 5.15% |
| AGGT | 4.63% |
| TCCT | 3.86% |
| ATCT | 3.72% |
| AGGA | 3.39% |
| GCCT | 3.12% |
| CCCT | 2.71% |
| AGCT | 2.55% |
| TTCT | 2.37% |
| AGGC | 2.31% |
| AGAT | 2.07% |
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