Input data and parameters 

Input

Analysis date: Tue Oct 31 10:05:23 GMT 2023
BAM file: SRX7354374.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): 52,753,753 / 52,708,450
Number of aligned pairs (without duplicates): 52,702,661
Total number of alignments: 112,225,788
Number of secondary alignments: 6,763,585
Number of non-unique alignments: 11,409,808
Aligned to genes: 86,304,505
Ambiguous alignments: 313,791
No feature assigned: 13,818,934
Missing chromosome in annotation: 378,750
Not aligned: 5,949,749

Reads genomic origin

Exonic: 86,304,505 / 86.2%
Intronic: 9,343,897 / 9.33%
Intergenic: 4,475,037 / 4.47%
Intronic/intergenic overlapping exon: 3,486,704 / 3.48%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.18
5'-3' bias: 1.74

Junction analysis

Reads at junctions: 28,622,176
ACCT 5.36%
AGGT 4.63%
ATCT 3.61%
AGGA 3.56%
TCCT 3.34%
GCCT 3.19%
AGCT 2.72%
AGGC 2.37%
CCCT 2.33%
AGAT 2.27%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis