Input data and parameters 

Input

Analysis date: Tue Oct 31 09:13:54 GMT 2023
BAM file: SRX7354311.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): 52,882,898 / 52,839,827
Number of aligned pairs (without duplicates): 52,830,212
Total number of alignments: 127,120,041
Number of secondary alignments: 21,397,316
Number of non-unique alignments: 21,954,087
Aligned to genes: 88,066,390
Ambiguous alignments: 383,625
No feature assigned: 8,867,694
Missing chromosome in annotation: 7,848,245
Not aligned: 3,512,865

Reads genomic origin

Exonic: 88,066,390 / 90.85%
Intronic: 5,110,156 / 5.27%
Intergenic: 3,757,538 / 3.88%
Intronic/intergenic overlapping exon: 3,661,313 / 3.78%

Transcript coverage profile

5' bias: 0.14
3' bias: 0.14
5'-3' bias: 2.58

Junction analysis

Reads at junctions: 30,284,187
TCCT 4.72%
AGGT 4.64%
ACCT 4.63%
ATCT 3.71%
AGGA 3.37%
CCCT 2.73%
AGGC 2.46%
AGCT 2.18%
AGAC 1.93%
TTCT 1.88%
GCCT 1.87%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis