Input data and parameters
Input
Analysis date: | Sun Oct 29 11:43:18 GMT 2023 |
BAM file: | SRX7354089.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): | 39,245,384 / 39,207,108 |
Number of aligned pairs (without duplicates): | 39,202,588 |
Total number of alignments: | 83,230,503 |
Number of secondary alignments: | 4,778,011 |
Number of non-unique alignments: | 8,038,896 |
Aligned to genes: | 65,922,604 |
Ambiguous alignments: | 206,603 |
No feature assigned: | 8,718,287 |
Missing chromosome in annotation: | 344,113 |
Not aligned: | 8,364,196 |
Reads genomic origin
Exonic: | 65,922,604 / 88.32% |
Intronic: | 5,360,025 / 7.18% |
Intergenic: | 3,358,262 / 4.5% |
Intronic/intergenic overlapping exon: | 2,750,948 / 3.69% |
Transcript coverage profile
5' bias: | 0.32 |
3' bias: | 0.18 |
5'-3' bias: | 1.99 |
Junction analysis
Reads at junctions: | 19,881,417 |
ACCT | 5.26% |
AGGT | 4.68% |
ATCT | 4.07% |
TCCT | 3.51% |
AGGA | 3.45% |
GCCT | 3.22% |
AGCT | 2.61% |
CCCT | 2.54% |
AGGC | 2.34% |
TTCT | 2.2% |
AGAT | 2.13% |