Input data and parameters
Input
Analysis date: | Mon Oct 30 23:20:47 GMT 2023 |
BAM file: | SRX7354221.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): | 36,503,748 / 36,481,069 |
Number of aligned pairs (without duplicates): | 36,477,526 |
Total number of alignments: | 77,082,466 |
Number of secondary alignments: | 4,097,649 |
Number of non-unique alignments: | 6,695,566 |
Aligned to genes: | 60,699,706 |
Ambiguous alignments: | 223,256 |
No feature assigned: | 9,153,955 |
Missing chromosome in annotation: | 309,983 |
Not aligned: | 3,474,061 |
Reads genomic origin
Exonic: | 60,699,706 / 86.9% |
Intronic: | 6,317,388 / 9.04% |
Intergenic: | 2,836,567 / 4.06% |
Intronic/intergenic overlapping exon: | 2,454,342 / 3.51% |
Transcript coverage profile
5' bias: | 0.37 |
3' bias: | 0.18 |
5'-3' bias: | 1.89 |
Junction analysis
Reads at junctions: | 19,739,845 |
ACCT | 5.43% |
AGGT | 4.8% |
AGGA | 3.59% |
ATCT | 3.55% |
TCCT | 3.37% |
GCCT | 3.06% |
AGCT | 2.78% |
AGGC | 2.44% |
CCCT | 2.35% |
AGAT | 2.29% |
TTCT | 2.27% |