Input data and parameters
Input
Analysis date: | Sun Oct 29 01:30:27 GMT 2023 |
BAM file: | SRX7354054.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): | 27,832,575 / 27,813,922 |
Number of aligned pairs (without duplicates): | 27,810,680 |
Total number of alignments: | 58,945,548 |
Number of secondary alignments: | 3,299,051 |
Number of non-unique alignments: | 5,345,654 |
Aligned to genes: | 47,396,075 |
Ambiguous alignments: | 166,979 |
No feature assigned: | 5,729,011 |
Missing chromosome in annotation: | 307,829 |
Not aligned: | 1,993,029 |
Reads genomic origin
Exonic: | 47,396,075 / 89.22% |
Intronic: | 3,666,499 / 6.9% |
Intergenic: | 2,062,512 / 3.88% |
Intronic/intergenic overlapping exon: | 1,909,329 / 3.59% |
Transcript coverage profile
5' bias: | 0.37 |
3' bias: | 0.18 |
5'-3' bias: | 2.2 |
Junction analysis
Reads at junctions: | 14,714,661 |
ACCT | 5.54% |
AGGT | 4.61% |
ATCT | 3.81% |
TCCT | 3.55% |
GCCT | 3.51% |
AGGA | 3.34% |
CCCT | 2.5% |
AGCT | 2.49% |
TTCT | 2.36% |
AGGC | 2.34% |
AGAT | 2.01% |