Input data and parameters 

Input

Analysis date: Sun Oct 29 01:43:33 GMT 2023
BAM file: SRX7354079.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): 50,951,465 / 50,874,826
Number of aligned pairs (without duplicates): 50,867,287
Total number of alignments: 110,182,154
Number of secondary alignments: 8,355,863
Number of non-unique alignments: 14,510,627
Aligned to genes: 83,973,803
Ambiguous alignments: 284,278
No feature assigned: 10,995,644
Missing chromosome in annotation: 417,802
Not aligned: 11,835,941

Reads genomic origin

Exonic: 83,973,803 / 88.42%
Intronic: 6,604,481 / 6.95%
Intergenic: 4,391,163 / 4.62%
Intronic/intergenic overlapping exon: 3,995,089 / 4.21%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.24
5'-3' bias: 1.78

Junction analysis

Reads at junctions: 27,214,838
ACCT 5.45%
AGGT 4.49%
GCCT 3.65%
ATCT 3.64%
TCCT 3.41%
AGGA 3.31%
AGCT 2.68%
TTCT 2.51%
CCCT 2.49%
AGGC 2.35%
AGAT 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