Input data and parameters
Input
Analysis date: | Sun Oct 29 12:14:38 GMT 2023 |
BAM file: | SRX7354131.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): | 57,394,953 / 57,353,995 |
Number of aligned pairs (without duplicates): | 57,348,042 |
Total number of alignments: | 122,185,770 |
Number of secondary alignments: | 7,436,822 |
Number of non-unique alignments: | 12,412,179 |
Aligned to genes: | 92,062,463 |
Ambiguous alignments: | 314,697 |
No feature assigned: | 16,915,742 |
Missing chromosome in annotation: | 480,689 |
Not aligned: | 4,107,292 |
Reads genomic origin
Exonic: | 92,062,463 / 84.48% |
Intronic: | 11,877,722 / 10.9% |
Intergenic: | 5,038,020 / 4.62% |
Intronic/intergenic overlapping exon: | 3,915,960 / 3.59% |
Transcript coverage profile
5' bias: | 0.3 |
3' bias: | 0.18 |
5'-3' bias: | 1.85 |
Junction analysis
Reads at junctions: | 28,412,628 |
ACCT | 5.34% |
AGGT | 4.66% |
ATCT | 3.67% |
AGGA | 3.66% |
TCCT | 3.51% |
GCCT | 3.18% |
AGCT | 2.65% |
CCCT | 2.45% |
AGAT | 2.39% |
AGGC | 2.37% |
TTCT | 2.16% |