Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:43:55 GMT 2023 |
| BAM file: | SRX7354087.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): | 65,372,906 / 65,284,004 |
| Number of aligned pairs (without duplicates): | 65,276,619 |
| Total number of alignments: | 138,820,358 |
| Number of secondary alignments: | 8,163,448 |
| Number of non-unique alignments: | 13,084,272 |
| Aligned to genes: | 101,575,831 |
| Ambiguous alignments: | 363,951 |
| No feature assigned: | 22,957,720 |
| Missing chromosome in annotation: | 838,584 |
| Not aligned: | 10,776,242 |
Reads genomic origin
| Exonic: | 101,575,831 / 81.57% |
| Intronic: | 13,699,127 / 11% |
| Intergenic: | 9,258,593 / 7.43% |
| Intronic/intergenic overlapping exon: | 5,146,393 / 4.13% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.69 |
Junction analysis
| Reads at junctions: | 33,498,862 |
| ACCT | 4.99% |
| AGGT | 4.79% |
| TCCT | 3.69% |
| ATCT | 3.57% |
| AGGA | 3.45% |
| GCCT | 3.17% |
| CCCT | 2.79% |
| AGCT | 2.76% |
| AGGC | 2.53% |
| TTCT | 2.01% |
| AGAT | 2.01% |
.png)
.png)
.png)
