Input data and parameters
Input
| Analysis date: | Sat Mar 26 18:12:42 GMT 2022 |
| BAM file: | juvenile.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): | 210,304,183 / 210,278,128 |
| Number of aligned pairs (without duplicates): | 210,168,928 |
| Total number of alignments: | 461,972,496 |
| Number of secondary alignments: | 41,390,185 |
| Number of non-unique alignments: | 69,977,096 |
| Aligned to genes: | 100,442,329 |
| Ambiguous alignments: | 9,449 |
| No feature assigned: | 291,543,622 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 100,442,329 / 25.62% |
| Intronic: | 68,230,885 / 17.41% |
| Intergenic: | 223,312,737 / 56.97% |
| Intronic/intergenic overlapping exon: | 30,291,613 / 7.73% |
Transcript coverage profile
| 5' bias: | 0.55 |
| 3' bias: | 0.58 |
| 5'-3' bias: | 0.93 |
Junction analysis
| Reads at junctions: | 119,877,069 |
| AGGT | 6.36% |
| ACCT | 5.5% |
| AGAT | 3.2% |
| TCCT | 3.14% |
| ATCT | 2.92% |
| AGCT | 2.52% |
| AGGA | 2.33% |
| AGAA | 1.99% |
| AGGG | 1.89% |
| TTCT | 1.82% |
| AGGC | 1.77% |
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