Input data and parameters 

Input

Analysis date: Tue Oct 31 09:52:48 GMT 2023
BAM file: SRX7354328.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): 41,207,039 / 41,077,532
Number of aligned pairs (without duplicates): 41,055,031
Total number of alignments: 88,617,064
Number of secondary alignments: 6,332,493
Number of non-unique alignments: 10,661,547
Aligned to genes: 69,797,539
Ambiguous alignments: 262,704
No feature assigned: 7,575,172
Missing chromosome in annotation: 320,102
Not aligned: 7,747,195

Reads genomic origin

Exonic: 69,797,539 / 90.21%
Intronic: 4,926,732 / 6.37%
Intergenic: 2,648,440 / 3.42%
Intronic/intergenic overlapping exon: 2,981,072 / 3.85%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.21
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 22,527,070
ACCT 5.05%
AGGT 4.74%
ATCT 4.3%
TCCT 3.7%
AGGA 3.43%
GCCT 2.93%
CCCT 2.63%
AGCT 2.37%
AGGC 2.23%
TTCT 2.18%
AGAA 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis