Input data and parameters
Input
Analysis date: | Sun Oct 29 02:09:33 GMT 2023 |
BAM file: | SRX7354097.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): | 73,092,226 / 73,052,131 |
Number of aligned pairs (without duplicates): | 73,036,537 |
Total number of alignments: | 158,509,928 |
Number of secondary alignments: | 12,365,571 |
Number of non-unique alignments: | 19,498,233 |
Aligned to genes: | 125,137,379 |
Ambiguous alignments: | 555,416 |
No feature assigned: | 11,929,206 |
Missing chromosome in annotation: | 1,389,694 |
Not aligned: | 5,120,351 |
Reads genomic origin
Exonic: | 125,137,379 / 91.3% |
Intronic: | 6,781,220 / 4.95% |
Intergenic: | 5,147,986 / 3.76% |
Intronic/intergenic overlapping exon: | 5,820,628 / 4.25% |
Transcript coverage profile
5' bias: | 0.1 |
3' bias: | 0.12 |
5'-3' bias: | 1.94 |
Junction analysis
Reads at junctions: | 43,410,114 |
ACCT | 5.2% |
TCCT | 5.03% |
ATCT | 4.59% |
AGGT | 4.37% |
CCCT | 3.51% |
AGGA | 2.88% |
GCCT | 2.41% |
AGGC | 2.35% |
TTCT | 2.28% |
AGCT | 1.97% |
AGAC | 1.87% |