Input data and parameters 

Input

Analysis date: Tue Oct 31 09:31:49 GMT 2023
BAM file: SRX7354329.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): 31,873,611 / 31,832,867
Number of aligned pairs (without duplicates): 31,828,146
Total number of alignments: 67,833,400
Number of secondary alignments: 4,126,922
Number of non-unique alignments: 6,949,009
Aligned to genes: 53,035,953
Ambiguous alignments: 164,404
No feature assigned: 7,415,634
Missing chromosome in annotation: 268,400
Not aligned: 14,819,606

Reads genomic origin

Exonic: 53,035,953 / 87.73%
Intronic: 4,349,125 / 7.19%
Intergenic: 3,066,509 / 5.07%
Intronic/intergenic overlapping exon: 1,909,839 / 3.16%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.16
5'-3' bias: 2.4

Junction analysis

Reads at junctions: 16,301,757
ACCT 5.32%
AGGT 4.78%
ATCT 3.79%
AGGA 3.68%
TCCT 3.41%
GCCT 2.97%
AGCT 2.71%
CCCT 2.45%
AGGC 2.4%
AGAT 2.35%
TTCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis