Input data and parameters 

Input

Analysis date: Tue Oct 31 09:54:33 GMT 2023
BAM file: SRX7354356.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): 35,152,075 / 35,130,677
Number of aligned pairs (without duplicates): 35,127,068
Total number of alignments: 74,951,306
Number of secondary alignments: 4,668,554
Number of non-unique alignments: 7,834,381
Aligned to genes: 58,824,585
Ambiguous alignments: 202,820
No feature assigned: 7,820,388
Missing chromosome in annotation: 269,132
Not aligned: 4,177,960

Reads genomic origin

Exonic: 58,824,585 / 88.27%
Intronic: 5,233,329 / 7.85%
Intergenic: 2,587,059 / 3.88%
Intronic/intergenic overlapping exon: 2,129,191 / 3.19%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.15
5'-3' bias: 2.42

Junction analysis

Reads at junctions: 17,972,173
ACCT 5.33%
AGGT 4.7%
ATCT 3.62%
AGGA 3.6%
TCCT 3.51%
GCCT 3.07%
AGCT 2.65%
AGGC 2.34%
CCCT 2.28%
AGAT 2.27%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis