Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:07:09 GMT 2023 |
| BAM file: | SRX7354144.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): | 32,687,334 / 32,659,377 |
| Number of aligned pairs (without duplicates): | 32,655,055 |
| Total number of alignments: | 69,605,442 |
| Number of secondary alignments: | 4,258,731 |
| Number of non-unique alignments: | 7,112,599 |
| Aligned to genes: | 53,017,987 |
| Ambiguous alignments: | 186,025 |
| No feature assigned: | 9,034,700 |
| Missing chromosome in annotation: | 254,131 |
| Not aligned: | 5,777,527 |
Reads genomic origin
| Exonic: | 53,017,987 / 85.44% |
| Intronic: | 6,192,600 / 9.98% |
| Intergenic: | 2,842,100 / 4.58% |
| Intronic/intergenic overlapping exon: | 2,276,300 / 3.67% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.88 |
Junction analysis
| Reads at junctions: | 17,942,087 |
| ACCT | 5.54% |
| AGGT | 4.78% |
| AGGA | 3.64% |
| ATCT | 3.58% |
| TCCT | 3.38% |
| GCCT | 3.18% |
| AGCT | 2.71% |
| AGAT | 2.44% |
| CCCT | 2.43% |
| AGGC | 2.38% |
| TTCT | 2.17% |
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