Input data and parameters
Input
Analysis date: | Mon Oct 30 20:30:08 GMT 2023 |
BAM file: | SRX7354249.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): | 31,585,753 / 31,558,365 |
Number of aligned pairs (without duplicates): | 31,547,007 |
Total number of alignments: | 68,219,661 |
Number of secondary alignments: | 5,075,543 |
Number of non-unique alignments: | 7,991,039 |
Aligned to genes: | 52,906,605 |
Ambiguous alignments: | 242,653 |
No feature assigned: | 6,524,392 |
Missing chromosome in annotation: | 554,972 |
Not aligned: | 1,485,008 |
Reads genomic origin
Exonic: | 52,906,605 / 89.02% |
Intronic: | 4,419,013 / 7.44% |
Intergenic: | 2,105,379 / 3.54% |
Intronic/intergenic overlapping exon: | 2,993,674 / 5.04% |
Transcript coverage profile
5' bias: | 0.23 |
3' bias: | 0.23 |
5'-3' bias: | 1.85 |
Junction analysis
Reads at junctions: | 19,088,914 |
ACCT | 4.99% |
AGGT | 4.7% |
ATCT | 4.08% |
TCCT | 4.01% |
AGGA | 3.19% |
CCCT | 3.03% |
GCCT | 2.86% |
AGGC | 2.48% |
AGCT | 2.41% |
TTCT | 2.1% |
AGAA | 1.88% |