Input data and parameters 

Input

Analysis date: Tue Oct 31 15:43:35 GMT 2023
BAM file: SRX7354404.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): 45,243,192 / 45,182,727
Number of aligned pairs (without duplicates): 45,145,836
Total number of alignments: 97,423,567
Number of secondary alignments: 6,997,648
Number of non-unique alignments: 11,808,304
Aligned to genes: 75,937,352
Ambiguous alignments: 312,660
No feature assigned: 8,921,364
Missing chromosome in annotation: 443,887
Not aligned: 4,794,239

Reads genomic origin

Exonic: 75,937,352 / 89.49%
Intronic: 5,747,869 / 6.77%
Intergenic: 3,173,495 / 3.74%
Intronic/intergenic overlapping exon: 3,901,100 / 4.6%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.22
5'-3' bias: 2.03

Junction analysis

Reads at junctions: 30,011,382
ACCT 5.43%
AGGT 4.53%
ATCT 4.26%
TCCT 4.06%
GCCT 3.42%
AGGA 3.05%
CCCT 2.86%
AGCT 2.45%
AGGC 2.45%
TTCT 2.31%
AGAA 1.74%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis