Input data and parameters 

Input

Analysis date: Sun Oct 29 01:41:20 GMT 2023
BAM file: SRX7354117.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): 31,478,525 / 31,456,292
Number of aligned pairs (without duplicates): 31,453,213
Total number of alignments: 67,093,216
Number of secondary alignments: 4,158,399
Number of non-unique alignments: 6,775,395
Aligned to genes: 53,145,382
Ambiguous alignments: 181,085
No feature assigned: 6,589,258
Missing chromosome in annotation: 402,096
Not aligned: 1,585,659

Reads genomic origin

Exonic: 53,145,382 / 88.97%
Intronic: 4,412,444 / 7.39%
Intergenic: 2,176,814 / 3.64%
Intronic/intergenic overlapping exon: 2,071,045 / 3.47%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.21
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 18,158,070
ACCT 5.29%
AGGT 4.54%
ATCT 3.85%
GCCT 3.45%
AGGA 3.38%
TCCT 3.26%
AGCT 2.74%
CCCT 2.62%
TTCT 2.44%
AGGC 2.29%
AGAT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis