Input data and parameters 

Input

Analysis date: Mon Oct 30 11:13:56 GMT 2023
BAM file: SRX7354210.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): 44,890,175 / 44,872,580
Number of aligned pairs (without duplicates): 44,865,272
Total number of alignments: 97,973,167
Number of secondary alignments: 8,210,412
Number of non-unique alignments: 12,356,701
Aligned to genes: 76,578,948
Ambiguous alignments: 282,933
No feature assigned: 7,697,755
Missing chromosome in annotation: 1,056,830
Not aligned: 3,036,901

Reads genomic origin

Exonic: 76,578,948 / 90.87%
Intronic: 4,940,927 / 5.86%
Intergenic: 2,756,828 / 3.27%
Intronic/intergenic overlapping exon: 3,620,386 / 4.3%

Transcript coverage profile

5' bias: 0.15
3' bias: 0.16
5'-3' bias: 2.15

Junction analysis

Reads at junctions: 31,604,985
ACCT 5.28%
TCCT 4.57%
AGGT 4.48%
ATCT 4.35%
AGGA 3.02%
CCCT 2.7%
GCCT 2.45%
AGGC 2.23%
AGCT 2%
TTCT 1.94%
AACT 1.83%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis