Input data and parameters 

Input

Analysis date: Sun Oct 29 13:13:37 GMT 2023
BAM file: SRX7354155.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): 68,887,389 / 68,839,702
Number of aligned pairs (without duplicates): 68,835,029
Total number of alignments: 148,517,519
Number of secondary alignments: 10,790,428
Number of non-unique alignments: 15,869,265
Aligned to genes: 108,680,798
Ambiguous alignments: 413,738
No feature assigned: 21,782,492
Missing chromosome in annotation: 1,771,226
Not aligned: 3,964,535

Reads genomic origin

Exonic: 108,680,798 / 83.3%
Intronic: 12,698,113 / 9.73%
Intergenic: 9,084,379 / 6.96%
Intronic/intergenic overlapping exon: 5,075,380 / 3.89%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.37
5'-3' bias: 1.51

Junction analysis

Reads at junctions: 41,706,548
ACCT 5.01%
AGGT 4.68%
TCCT 3.91%
ATCT 3.66%
GCCT 3.29%
AGGA 3.21%
AGCT 2.73%
CCCT 2.71%
TTCT 2.48%
AGGC 2.45%
AGAT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis