Input data and parameters 

Input

Analysis date: Sun Oct 29 01:18:57 GMT 2023
BAM file: SRX7354049.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): 44,037,452 / 44,003,256
Number of aligned pairs (without duplicates): 43,997,586
Total number of alignments: 93,616,528
Number of secondary alignments: 5,575,820
Number of non-unique alignments: 9,305,861
Aligned to genes: 70,431,424
Ambiguous alignments: 246,340
No feature assigned: 13,279,447
Missing chromosome in annotation: 353,456
Not aligned: 4,901,880

Reads genomic origin

Exonic: 70,431,424 / 84.14%
Intronic: 10,164,642 / 12.14%
Intergenic: 3,114,805 / 3.72%
Intronic/intergenic overlapping exon: 2,983,825 / 3.56%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.17
5'-3' bias: 2.31

Junction analysis

Reads at junctions: 22,475,219
ACCT 5.2%
AGGT 4.82%
AGGA 3.75%
ATCT 3.61%
TCCT 3.54%
GCCT 2.77%
AGCT 2.76%
CCCT 2.4%
AGGC 2.38%
AGAT 2.37%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis