Input data and parameters
Input
Analysis date: | Tue Oct 31 09:54:21 GMT 2023 |
BAM file: | SRX7354395.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): | 32,326,028 / 32,242,180 |
Number of aligned pairs (without duplicates): | 32,236,626 |
Total number of alignments: | 68,647,743 |
Number of secondary alignments: | 4,079,535 |
Number of non-unique alignments: | 6,803,335 |
Aligned to genes: | 53,048,704 |
Ambiguous alignments: | 190,310 |
No feature assigned: | 8,348,918 |
Missing chromosome in annotation: | 256,476 |
Not aligned: | 6,592,144 |
Reads genomic origin
Exonic: | 53,048,704 / 86.4% |
Intronic: | 5,470,628 / 8.91% |
Intergenic: | 2,878,290 / 4.69% |
Intronic/intergenic overlapping exon: | 2,176,128 / 3.54% |
Transcript coverage profile
5' bias: | 0.32 |
3' bias: | 0.18 |
5'-3' bias: | 1.88 |
Junction analysis
Reads at junctions: | 16,371,131 |
ACCT | 5.31% |
AGGT | 4.78% |
ATCT | 3.69% |
AGGA | 3.55% |
TCCT | 3.36% |
GCCT | 3.2% |
AGCT | 2.67% |
AGGC | 2.43% |
CCCT | 2.42% |
AGAT | 2.3% |
TTCT | 2.27% |