Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:44:39 GMT 2023 |
| BAM file: | SRX7354164.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): | 41,627,353 / 41,601,806 |
| Number of aligned pairs (without duplicates): | 41,597,357 |
| Total number of alignments: | 88,640,387 |
| Number of secondary alignments: | 5,411,228 |
| Number of non-unique alignments: | 9,007,875 |
| Aligned to genes: | 70,031,403 |
| Ambiguous alignments: | 239,677 |
| No feature assigned: | 8,960,517 |
| Missing chromosome in annotation: | 400,915 |
| Not aligned: | 3,569,389 |
Reads genomic origin
| Exonic: | 70,031,403 / 88.66% |
| Intronic: | 5,784,392 / 7.32% |
| Intergenic: | 3,176,125 / 4.02% |
| Intronic/intergenic overlapping exon: | 2,752,850 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.91 |
Junction analysis
| Reads at junctions: | 21,181,027 |
| ACCT | 5.16% |
| AGGT | 4.66% |
| ATCT | 3.62% |
| TCCT | 3.59% |
| AGGA | 3.58% |
| GCCT | 3% |
| AGCT | 2.73% |
| CCCT | 2.41% |
| AGGC | 2.34% |
| TTCT | 2.2% |
| AGAT | 2.18% |
.png)
.png)
.png)
