Input data and parameters 

Input

Analysis date: Sun Oct 29 12:46:15 GMT 2023
BAM file: SRX7354172.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): 31,107,863 / 31,086,424
Number of aligned pairs (without duplicates): 31,082,532
Total number of alignments: 65,994,299
Number of secondary alignments: 3,800,012
Number of non-unique alignments: 6,251,368
Aligned to genes: 51,897,122
Ambiguous alignments: 175,611
No feature assigned: 7,350,117
Missing chromosome in annotation: 320,081
Not aligned: 3,049,015

Reads genomic origin

Exonic: 51,897,122 / 87.59%
Intronic: 4,787,409 / 8.08%
Intergenic: 2,562,708 / 4.33%
Intronic/intergenic overlapping exon: 2,136,688 / 3.61%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.19
5'-3' bias: 2.17

Junction analysis

Reads at junctions: 15,742,232
ACCT 5.47%
AGGT 4.76%
ATCT 3.71%
AGGA 3.54%
TCCT 3.49%
GCCT 3.08%
AGCT 2.71%
CCCT 2.45%
AGGC 2.36%
AGAT 2.21%
TTCT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis