Input data and parameters
Input
| Analysis date: | Fri Mar 25 18:21:14 GMT 2022 |
| BAM file: | heart.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.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): | 66,316,235 / 66,313,855 |
| Number of aligned pairs (without duplicates): | 66,278,065 |
| Total number of alignments: | 144,781,076 |
| Number of secondary alignments: | 12,150,986 |
| Number of non-unique alignments: | 20,639,611 |
| Aligned to genes: | 40,861,023 |
| Ambiguous alignments: | 89 |
| No feature assigned: | 83,280,353 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 40,861,023 / 32.91% |
| Intronic: | 21,741,193 / 17.51% |
| Intergenic: | 61,539,160 / 49.57% |
| Intronic/intergenic overlapping exon: | 8,843,360 / 7.12% |
Transcript coverage profile
| 5' bias: | 0.6 |
| 3' bias: | 0.53 |
| 5'-3' bias: | 1.05 |
Junction analysis
| Reads at junctions: | 40,179,761 |
| AGGT | 5.99% |
| ACCT | 5.56% |
| AGAT | 3.11% |
| CCCT | 2.99% |
| ATCT | 2.99% |
| TCCT | 2.97% |
| AGGA | 2.6% |
| AGCT | 2.37% |
| AGAA | 2.13% |
| AGGC | 1.93% |
| AGGG | 1.8% |
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