Input data and parameters
Input
Analysis date: | Sun Oct 29 01:56:52 GMT 2023 |
BAM file: | SRX7354096.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): | 55,529,928 / 55,490,400 |
Number of aligned pairs (without duplicates): | 55,484,401 |
Total number of alignments: | 119,426,315 |
Number of secondary alignments: | 8,405,987 |
Number of non-unique alignments: | 13,986,788 |
Aligned to genes: | 92,240,458 |
Ambiguous alignments: | 319,090 |
No feature assigned: | 12,300,535 |
Missing chromosome in annotation: | 579,444 |
Not aligned: | 5,226,298 |
Reads genomic origin
Exonic: | 92,240,458 / 88.23% |
Intronic: | 6,870,606 / 6.57% |
Intergenic: | 5,429,929 / 5.19% |
Intronic/intergenic overlapping exon: | 3,443,769 / 3.29% |
Transcript coverage profile
5' bias: | 0.28 |
3' bias: | 0.2 |
5'-3' bias: | 1.85 |
Junction analysis
Reads at junctions: | 29,007,850 |
ACCT | 5.26% |
AGGT | 4.91% |
AGGA | 3.65% |
TCCT | 3.64% |
ATCT | 3.52% |
GCCT | 2.73% |
AGCT | 2.68% |
CCCT | 2.53% |
AGGC | 2.41% |
TTCT | 2.25% |
AGAT | 2.17% |