Input data and parameters 

Input

Analysis date: Mon Oct 30 23:03:01 GMT 2023
BAM file: SRX7354235.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): 44,093,041 / 44,050,564
Number of aligned pairs (without duplicates): 44,021,315
Total number of alignments: 95,133,010
Number of secondary alignments: 6,989,405
Number of non-unique alignments: 11,001,785
Aligned to genes: 73,772,847
Ambiguous alignments: 305,748
No feature assigned: 9,195,992
Missing chromosome in annotation: 856,638
Not aligned: 2,631,765

Reads genomic origin

Exonic: 73,772,847 / 88.92%
Intronic: 6,043,231 / 7.28%
Intergenic: 3,152,761 / 3.8%
Intronic/intergenic overlapping exon: 3,703,126 / 4.46%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.29
5'-3' bias: 1.64

Junction analysis

Reads at junctions: 25,856,141
ACCT 5.52%
AGGT 4.55%
TCCT 3.87%
ATCT 3.8%
GCCT 3.69%
AGGA 3.05%
CCCT 2.78%
AGCT 2.64%
AGGC 2.37%
TTCT 2.29%
AGAT 1.8%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis