Input data and parameters 

Input

Analysis date: Mon Oct 30 11:19:59 GMT 2023
BAM file: SRX7354180.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): 31,556,184 / 31,538,928
Number of aligned pairs (without duplicates): 31,535,627
Total number of alignments: 67,075,290
Number of secondary alignments: 3,980,178
Number of non-unique alignments: 6,581,649
Aligned to genes: 52,544,695
Ambiguous alignments: 190,639
No feature assigned: 7,484,759
Missing chromosome in annotation: 273,548
Not aligned: 2,198,286

Reads genomic origin

Exonic: 52,544,695 / 87.53%
Intronic: 5,401,780 / 9%
Intergenic: 2,082,979 / 3.47%
Intronic/intergenic overlapping exon: 2,081,688 / 3.47%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.21
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 18,351,268
ACCT 5.35%
AGGT 4.73%
AGGA 3.64%
ATCT 3.47%
TCCT 3.34%
GCCT 3.29%
AGCT 2.82%
CCCT 2.45%
AGGC 2.42%
AGAT 2.33%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis