Input data and parameters
Input
Analysis date: | Tue Oct 31 15:49:10 GMT 2023 |
BAM file: | SRX7354414.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): | 58,554,816 / 58,525,802 |
Number of aligned pairs (without duplicates): | 58,515,123 |
Total number of alignments: | 132,247,847 |
Number of secondary alignments: | 15,167,229 |
Number of non-unique alignments: | 18,913,450 |
Aligned to genes: | 95,729,342 |
Ambiguous alignments: | 565,887 |
No feature assigned: | 13,024,829 |
Missing chromosome in annotation: | 4,014,339 |
Not aligned: | 3,035,444 |
Reads genomic origin
Exonic: | 95,729,342 / 88.02% |
Intronic: | 9,685,508 / 8.91% |
Intergenic: | 3,339,321 / 3.07% |
Intronic/intergenic overlapping exon: | 5,609,166 / 5.16% |
Transcript coverage profile
5' bias: | 0.22 |
3' bias: | 0.16 |
5'-3' bias: | 1.92 |
Junction analysis
Reads at junctions: | 37,442,004 |
ACCT | 4.87% |
TCCT | 4.78% |
ATCT | 4.53% |
AGGT | 4.44% |
CCCT | 3.53% |
AGGA | 3.46% |
GCCT | 3.06% |
AGCT | 2.15% |
AGGC | 2.09% |
TTCT | 2.04% |
AGAA | 1.8% |