Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:43:00 GMT 2023 |
| BAM file: | SRX7354153.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): | 59,193,792 / 59,148,949 |
| Number of aligned pairs (without duplicates): | 59,143,194 |
| Total number of alignments: | 125,818,125 |
| Number of secondary alignments: | 7,475,384 |
| Number of non-unique alignments: | 12,439,347 |
| Aligned to genes: | 97,808,259 |
| Ambiguous alignments: | 327,551 |
| No feature assigned: | 14,719,792 |
| Missing chromosome in annotation: | 523,176 |
| Not aligned: | 4,212,999 |
Reads genomic origin
| Exonic: | 97,808,259 / 86.92% |
| Intronic: | 9,256,216 / 8.23% |
| Intergenic: | 5,463,576 / 4.86% |
| Intronic/intergenic overlapping exon: | 4,035,873 / 3.59% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 29,515,488 |
| ACCT | 5.48% |
| AGGT | 4.65% |
| AGGA | 3.52% |
| ATCT | 3.46% |
| GCCT | 3.43% |
| TCCT | 3.28% |
| AGCT | 2.69% |
| CCCT | 2.43% |
| AGGC | 2.42% |
| TTCT | 2.29% |
| AGAT | 2.25% |
.png)
.png)
.png)
