Input data and parameters 

Input

Analysis date: Sun Oct 29 01:19:56 GMT 2023
BAM file: SRX7354088.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): 38,524,073 / 38,489,984
Number of aligned pairs (without duplicates): 38,453,304
Total number of alignments: 90,347,357
Number of secondary alignments: 13,333,300
Number of non-unique alignments: 18,998,700
Aligned to genes: 52,448,124
Ambiguous alignments: 224,684
No feature assigned: 16,104,246
Missing chromosome in annotation: 2,571,603
Not aligned: 4,378,773

Reads genomic origin

Exonic: 52,448,124 / 76.51%
Intronic: 7,240,639 / 10.56%
Intergenic: 8,863,607 / 12.93%
Intronic/intergenic overlapping exon: 4,240,578 / 6.19%

Transcript coverage profile

5' bias: 0.09
3' bias: 0.11
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 18,228,230
TCCT 8.44%
ATCT 6.04%
ACCT 4.78%
CCCT 4.3%
AGGT 3.34%
GTCT 3.28%
TCCG 3.19%
AGGA 2.76%
TTCT 2.42%
AGAC 2.09%
GCCT 1.93%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis