Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:09:10 GMT 2023 |
| BAM file: | SRX7354118.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): | 33,187,357 / 33,167,042 |
| Number of aligned pairs (without duplicates): | 33,164,393 |
| Total number of alignments: | 70,848,116 |
| Number of secondary alignments: | 4,493,717 |
| Number of non-unique alignments: | 7,428,085 |
| Aligned to genes: | 54,669,429 |
| Ambiguous alignments: | 216,937 |
| No feature assigned: | 8,252,466 |
| Missing chromosome in annotation: | 281,199 |
| Not aligned: | 1,640,041 |
Reads genomic origin
| Exonic: | 54,669,429 / 86.88% |
| Intronic: | 5,905,560 / 9.39% |
| Intergenic: | 2,346,906 / 3.73% |
| Intronic/intergenic overlapping exon: | 2,070,199 / 3.29% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.1 |
Junction analysis
| Reads at junctions: | 18,586,162 |
| ACCT | 5.22% |
| AGGT | 4.64% |
| ATCT | 3.73% |
| TCCT | 3.55% |
| AGGA | 3.55% |
| GCCT | 3.19% |
| AGCT | 2.69% |
| CCCT | 2.44% |
| AGGC | 2.42% |
| AGAT | 2.29% |
| TTCT | 2.14% |
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