Input data and parameters
Input
| Analysis date: | Fri Mar 25 22:21:15 GMT 2022 |
| BAM file: | larvae.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): | 44,605,420 / 44,607,755 |
| Number of aligned pairs (without duplicates): | 44,576,579 |
| Total number of alignments: | 98,429,234 |
| Number of secondary alignments: | 9,216,059 |
| Number of non-unique alignments: | 15,738,580 |
| Aligned to genes: | 24,515,604 |
| Ambiguous alignments: | 212 |
| No feature assigned: | 58,174,838 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 24,515,604 / 29.65% |
| Intronic: | 15,293,538 / 18.49% |
| Intergenic: | 42,881,300 / 51.86% |
| Intronic/intergenic overlapping exon: | 6,829,552 / 8.26% |
Transcript coverage profile
| 5' bias: | 0.54 |
| 3' bias: | 0.56 |
| 5'-3' bias: | 0.94 |
Junction analysis
| Reads at junctions: | 27,805,433 |
| AGGT | 5.86% |
| ACCT | 5.18% |
| ATCT | 3.03% |
| TCCT | 2.98% |
| AGAT | 2.86% |
| AGCT | 2.29% |
| AGGA | 2.23% |
| TTCT | 1.78% |
| GCCT | 1.73% |
| AGGC | 1.66% |
| ACCA | 1.56% |
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