Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:48:42 GMT 2023 |
| BAM file: | SRX7354157.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): | 37,416,554 / 37,380,459 |
| Number of aligned pairs (without duplicates): | 37,376,452 |
| Total number of alignments: | 79,494,439 |
| Number of secondary alignments: | 4,697,426 |
| Number of non-unique alignments: | 7,798,287 |
| Aligned to genes: | 63,881,160 |
| Ambiguous alignments: | 221,293 |
| No feature assigned: | 7,274,929 |
| Missing chromosome in annotation: | 318,770 |
| Not aligned: | 4,679,217 |
Reads genomic origin
| Exonic: | 63,881,160 / 89.78% |
| Intronic: | 4,673,302 / 6.57% |
| Intergenic: | 2,601,627 / 3.66% |
| Intronic/intergenic overlapping exon: | 2,283,841 / 3.21% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.32 |
Junction analysis
| Reads at junctions: | 19,322,187 |
| ACCT | 5.46% |
| AGGT | 4.73% |
| ATCT | 3.57% |
| TCCT | 3.5% |
| AGGA | 3.47% |
| GCCT | 2.92% |
| TTCT | 2.74% |
| AGCT | 2.6% |
| AGGC | 2.4% |
| CCCT | 2.29% |
| AGAT | 2.16% |
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