Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:26:42 GMT 2023 |
| BAM file: | SRX7354309.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): | 38,648,215 / 38,624,577 |
| Number of aligned pairs (without duplicates): | 38,621,994 |
| Total number of alignments: | 82,481,459 |
| Number of secondary alignments: | 5,208,667 |
| Number of non-unique alignments: | 8,459,072 |
| Aligned to genes: | 64,561,136 |
| Ambiguous alignments: | 238,311 |
| No feature assigned: | 8,809,143 |
| Missing chromosome in annotation: | 413,797 |
| Not aligned: | 1,853,064 |
Reads genomic origin
| Exonic: | 64,561,136 / 87.99% |
| Intronic: | 6,167,367 / 8.41% |
| Intergenic: | 2,641,776 / 3.6% |
| Intronic/intergenic overlapping exon: | 2,247,279 / 3.06% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 2.03 |
Junction analysis
| Reads at junctions: | 20,588,908 |
| ACCT | 5.26% |
| AGGT | 4.76% |
| ATCT | 3.62% |
| AGGA | 3.59% |
| TCCT | 3.42% |
| GCCT | 3.15% |
| AGCT | 2.71% |
| CCCT | 2.56% |
| AGAT | 2.37% |
| AGGC | 2.36% |
| TTCT | 2.14% |
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