Input data and parameters 

Input

Analysis date: Sun Oct 29 01:47:20 GMT 2023
BAM file: SRX7354129.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): 37,846,508 / 37,803,185
Number of aligned pairs (without duplicates): 37,797,570
Total number of alignments: 81,001,076
Number of secondary alignments: 5,351,383
Number of non-unique alignments: 8,965,612
Aligned to genes: 61,492,000
Ambiguous alignments: 187,081
No feature assigned: 9,965,995
Missing chromosome in annotation: 390,388
Not aligned: 5,564,533

Reads genomic origin

Exonic: 61,492,000 / 86.05%
Intronic: 7,076,652 / 9.9%
Intergenic: 2,889,343 / 4.04%
Intronic/intergenic overlapping exon: 3,149,678 / 4.41%

Transcript coverage profile

5' bias: 0.44
3' bias: 0.18
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 21,948,690
ACCT 5.07%
AGGT 4.74%
ATCT 3.84%
TCCT 3.7%
AGGA 3.53%
AGCT 2.86%
GCCT 2.78%
AGGC 2.44%
CCCT 2.24%
TTCT 2.21%
AGAT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis