Input data and parameters
Input
| Analysis date: | Fri Mar 25 19:24:46 GMT 2022 |
| BAM file: | gonad.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): | 41,072,342 / 41,059,764 |
| Number of aligned pairs (without duplicates): | 41,017,159 |
| Total number of alignments: | 88,696,621 |
| Number of secondary alignments: | 6,564,515 |
| Number of non-unique alignments: | 11,027,828 |
| Aligned to genes: | 20,060,305 |
| Ambiguous alignments: | 100 |
| No feature assigned: | 57,608,388 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 20,060,305 / 25.83% |
| Intronic: | 16,547,866 / 21.31% |
| Intergenic: | 41,060,522 / 52.87% |
| Intronic/intergenic overlapping exon: | 5,329,654 / 6.86% |
Transcript coverage profile
| 5' bias: | 0.56 |
| 3' bias: | 0.53 |
| 5'-3' bias: | 1.06 |
Junction analysis
| Reads at junctions: | 28,937,910 |
| AGGT | 6.63% |
| ACCT | 4.92% |
| AGAT | 4.05% |
| AGTT | 3.22% |
| AGGA | 2.79% |
| ATCT | 2.74% |
| TCCT | 2.69% |
| AGGC | 2.55% |
| AGCT | 2.2% |
| AGAG | 2.12% |
| AGAA | 2.11% |
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