Input data and parameters 

Input

Analysis date: Sun Oct 29 01:36:23 GMT 2023
BAM file: SRX7354095.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): 31,744,963 / 31,719,529
Number of aligned pairs (without duplicates): 31,716,232
Total number of alignments: 67,734,611
Number of secondary alignments: 4,270,119
Number of non-unique alignments: 7,274,880
Aligned to genes: 52,251,375
Ambiguous alignments: 195,967
No feature assigned: 7,764,798
Missing chromosome in annotation: 247,591
Not aligned: 5,742,492

Reads genomic origin

Exonic: 52,251,375 / 87.06%
Intronic: 4,626,728 / 7.71%
Intergenic: 3,138,070 / 5.23%
Intronic/intergenic overlapping exon: 2,006,490 / 3.34%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.23
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 16,313,785
ACCT 5.44%
AGGT 4.68%
ATCT 3.61%
TCCT 3.49%
AGGA 3.46%
GCCT 3.35%
AGCT 2.72%
CCCT 2.66%
AGGC 2.41%
AGAT 2.21%
TTCT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis