Input data and parameters
Input
| Analysis date: | Tue Oct 31 15:47:32 GMT 2023 |
| BAM file: | SRX7354413.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): | 37,672,066 / 37,645,130 |
| Number of aligned pairs (without duplicates): | 37,639,967 |
| Total number of alignments: | 81,221,889 |
| Number of secondary alignments: | 5,904,693 |
| Number of non-unique alignments: | 9,958,286 |
| Aligned to genes: | 64,597,511 |
| Ambiguous alignments: | 252,937 |
| No feature assigned: | 5,993,999 |
| Missing chromosome in annotation: | 419,156 |
| Not aligned: | 2,696,946 |
Reads genomic origin
| Exonic: | 64,597,511 / 91.51% |
| Intronic: | 3,258,735 / 4.62% |
| Intergenic: | 2,735,264 / 3.87% |
| Intronic/intergenic overlapping exon: | 2,419,799 / 3.43% |
Transcript coverage profile
| 5' bias: | 0.18 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.8 |
Junction analysis
| Reads at junctions: | 19,443,398 |
| ACCT | 5.58% |
| TCCT | 4.75% |
| ATCT | 4.56% |
| AGGT | 4.38% |
| GCCT | 3.36% |
| AGGA | 2.96% |
| CCCT | 2.93% |
| TTCT | 2.27% |
| AGGC | 2.23% |
| AGCT | 2.18% |
| TCCC | 2.13% |
.png)
.png)
.png)
