Input data and parameters 

Input

Analysis date: Sun Oct 29 12:56:25 GMT 2023
BAM file: SRX7354127.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): 76,972,746 / 76,744,382
Number of aligned pairs (without duplicates): 76,733,279
Total number of alignments: 162,285,685
Number of secondary alignments: 8,568,557
Number of non-unique alignments: 13,615,947
Aligned to genes: 122,737,359
Ambiguous alignments: 447,878
No feature assigned: 24,530,821
Missing chromosome in annotation: 953,680
Not aligned: 21,205,742

Reads genomic origin

Exonic: 122,737,359 / 83.34%
Intronic: 17,092,562 / 11.61%
Intergenic: 7,438,259 / 5.05%
Intronic/intergenic overlapping exon: 6,544,453 / 4.44%

Transcript coverage profile

5' bias: 0.5
3' bias: 0.27
5'-3' bias: 1.66

Junction analysis

Reads at junctions: 51,067,445
ACCT 5.05%
AGGT 4.72%
ATCT 3.66%
TCCT 3.46%
AGGA 3.42%
GCCT 3.38%
AGCT 2.9%
CCCT 2.78%
AGGC 2.5%
AGAT 2.11%
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