Input data and parameters 

Input

Analysis date: Sun Oct 29 02:13:16 GMT 2023
BAM file: SRX7354062.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): 35,100,543 / 35,078,030
Number of aligned pairs (without duplicates): 35,074,928
Total number of alignments: 74,441,056
Number of secondary alignments: 4,262,483
Number of non-unique alignments: 7,147,751
Aligned to genes: 58,572,335
Ambiguous alignments: 206,695
No feature assigned: 8,265,005
Missing chromosome in annotation: 249,270
Not aligned: 3,702,861

Reads genomic origin

Exonic: 58,572,335 / 87.63%
Intronic: 5,749,844 / 8.6%
Intergenic: 2,515,161 / 3.76%
Intronic/intergenic overlapping exon: 2,197,145 / 3.29%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.17
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 18,437,877
ACCT 5.33%
AGGT 4.78%
ATCT 3.64%
AGGA 3.62%
TCCT 3.43%
GCCT 2.86%
AGCT 2.7%
TTCT 2.66%
AGAT 2.39%
AGGC 2.34%
CCCT 2.29%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis