Input data and parameters 

Input

Analysis date: Sun Oct 29 01:09:10 GMT 2023
BAM file: SRX7354118.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): 33,187,357 / 33,167,042
Number of aligned pairs (without duplicates): 33,164,393
Total number of alignments: 70,848,116
Number of secondary alignments: 4,493,717
Number of non-unique alignments: 7,428,085
Aligned to genes: 54,669,429
Ambiguous alignments: 216,937
No feature assigned: 8,252,466
Missing chromosome in annotation: 281,199
Not aligned: 1,640,041

Reads genomic origin

Exonic: 54,669,429 / 86.88%
Intronic: 5,905,560 / 9.39%
Intergenic: 2,346,906 / 3.73%
Intronic/intergenic overlapping exon: 2,070,199 / 3.29%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.19
5'-3' bias: 2.1

Junction analysis

Reads at junctions: 18,586,162
ACCT 5.22%
AGGT 4.64%
ATCT 3.73%
TCCT 3.55%
AGGA 3.55%
GCCT 3.19%
AGCT 2.69%
CCCT 2.44%
AGGC 2.42%
AGAT 2.29%
TTCT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis