Input data and parameters 

Input

Analysis date: Sun Oct 29 11:50:32 GMT 2023
BAM file: SRX7354082.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): 43,552,404 / 43,527,084
Number of aligned pairs (without duplicates): 43,519,417
Total number of alignments: 94,720,534
Number of secondary alignments: 7,641,046
Number of non-unique alignments: 10,881,474
Aligned to genes: 73,211,439
Ambiguous alignments: 290,581
No feature assigned: 8,947,647
Missing chromosome in annotation: 1,389,393
Not aligned: 2,262,624

Reads genomic origin

Exonic: 73,211,439 / 89.11%
Intronic: 5,979,141 / 7.28%
Intergenic: 2,968,506 / 3.61%
Intronic/intergenic overlapping exon: 3,178,387 / 3.87%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.23
5'-3' bias: 1.71

Junction analysis

Reads at junctions: 25,129,896
ACCT 5.34%
AGGT 4.27%
ATCT 4.21%
TCCT 4.17%
GCCT 3.55%
AGGA 3.06%
CCCT 2.59%
AGCT 2.44%
AGGC 2.31%
TTCT 2.19%
TCCC 1.9%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis