Input data and parameters 

Input

Analysis date: Tue Oct 31 09:54:21 GMT 2023
BAM file: SRX7354395.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): 32,326,028 / 32,242,180
Number of aligned pairs (without duplicates): 32,236,626
Total number of alignments: 68,647,743
Number of secondary alignments: 4,079,535
Number of non-unique alignments: 6,803,335
Aligned to genes: 53,048,704
Ambiguous alignments: 190,310
No feature assigned: 8,348,918
Missing chromosome in annotation: 256,476
Not aligned: 6,592,144

Reads genomic origin

Exonic: 53,048,704 / 86.4%
Intronic: 5,470,628 / 8.91%
Intergenic: 2,878,290 / 4.69%
Intronic/intergenic overlapping exon: 2,176,128 / 3.54%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.18
5'-3' bias: 1.88

Junction analysis

Reads at junctions: 16,371,131
ACCT 5.31%
AGGT 4.78%
ATCT 3.69%
AGGA 3.55%
TCCT 3.36%
GCCT 3.2%
AGCT 2.67%
AGGC 2.43%
CCCT 2.42%
AGAT 2.3%
TTCT 2.27%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis