Input data and parameters
Input
Analysis date: | Tue Oct 31 09:08:55 GMT 2023 |
BAM file: | SRX7354324.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): | 35,684,245 / 35,643,785 |
Number of aligned pairs (without duplicates): | 35,637,204 |
Total number of alignments: | 76,468,431 |
Number of secondary alignments: | 5,140,401 |
Number of non-unique alignments: | 8,989,813 |
Aligned to genes: | 60,862,463 |
Ambiguous alignments: | 215,512 |
No feature assigned: | 6,167,100 |
Missing chromosome in annotation: | 233,543 |
Not aligned: | 8,454,642 |
Reads genomic origin
Exonic: | 60,862,463 / 90.8% |
Intronic: | 3,335,197 / 4.98% |
Intergenic: | 2,831,903 / 4.22% |
Intronic/intergenic overlapping exon: | 2,751,990 / 4.11% |
Transcript coverage profile
5' bias: | 0.23 |
3' bias: | 0.19 |
5'-3' bias: | 1.9 |
Junction analysis
Reads at junctions: | 19,397,255 |
ACCT | 5.77% |
AGGT | 4.76% |
ATCT | 3.76% |
TCCT | 3.7% |
GCCT | 3.36% |
AGGA | 3.29% |
CCCT | 2.54% |
AGCT | 2.42% |
AGGC | 2.39% |
TTCT | 2.24% |
AGAT | 1.99% |