Input data and parameters 

Input

Analysis date: Sun Oct 29 01:52:43 GMT 2023
BAM file: SRX7354179.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): 36,770,141 / 36,731,997
Number of aligned pairs (without duplicates): 36,725,848
Total number of alignments: 78,096,453
Number of secondary alignments: 4,594,315
Number of non-unique alignments: 7,595,099
Aligned to genes: 61,051,104
Ambiguous alignments: 242,409
No feature assigned: 8,932,455
Missing chromosome in annotation: 275,386
Not aligned: 9,214,754

Reads genomic origin

Exonic: 61,051,104 / 87.24%
Intronic: 6,554,731 / 9.37%
Intergenic: 2,377,724 / 3.4%
Intronic/intergenic overlapping exon: 2,479,666 / 3.54%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.2
5'-3' bias: 2.07

Junction analysis

Reads at junctions: 23,169,242
ACCT 5.35%
AGGT 4.84%
AGGA 3.6%
ATCT 3.59%
TCCT 3.41%
GCCT 2.92%
AGCT 2.73%
CCCT 2.46%
AGGC 2.45%
AGAT 2.26%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis