Input data and parameters 

Input

Analysis date: Sun Oct 29 01:33:19 GMT 2023
BAM file: SRX7354135.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): 32,907,421 / 32,881,427
Number of aligned pairs (without duplicates): 32,877,541
Total number of alignments: 69,879,120
Number of secondary alignments: 4,090,272
Number of non-unique alignments: 6,767,039
Aligned to genes: 54,390,617
Ambiguous alignments: 186,582
No feature assigned: 8,221,258
Missing chromosome in annotation: 313,624
Not aligned: 5,995,000

Reads genomic origin

Exonic: 54,390,617 / 86.87%
Intronic: 5,504,175 / 8.79%
Intergenic: 2,717,083 / 4.34%
Intronic/intergenic overlapping exon: 2,218,566 / 3.54%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.2
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 17,881,100
ACCT 5.33%
AGGT 4.74%
ATCT 3.62%
AGGA 3.58%
TCCT 3.55%
GCCT 3.2%
AGCT 2.73%
CCCT 2.52%
AGGC 2.38%
AGAT 2.28%
TTCT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis