Input data and parameters
Input
Analysis date: | Tue Oct 31 17:40:58 GMT 2023 |
BAM file: | SRX7354394.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): | 35,968,400 / 35,877,814 |
Number of aligned pairs (without duplicates): | 35,830,916 |
Total number of alignments: | 77,017,935 |
Number of secondary alignments: | 5,171,721 |
Number of non-unique alignments: | 8,424,568 |
Aligned to genes: | 61,166,382 |
Ambiguous alignments: | 215,708 |
No feature assigned: | 6,728,245 |
Missing chromosome in annotation: | 483,032 |
Not aligned: | 6,342,294 |
Reads genomic origin
Exonic: | 61,166,382 / 90.09% |
Intronic: | 3,571,791 / 5.26% |
Intergenic: | 3,156,454 / 4.65% |
Intronic/intergenic overlapping exon: | 2,862,813 / 4.22% |
Transcript coverage profile
5' bias: | 0.36 |
3' bias: | 0.22 |
5'-3' bias: | 1.92 |
Junction analysis
Reads at junctions: | 20,547,149 |
ACCT | 5.52% |
TCCT | 4.63% |
ATCT | 4.32% |
AGGT | 4.29% |
GCCT | 3.54% |
AGGA | 2.89% |
CCCT | 2.63% |
AGCT | 2.38% |
AGGC | 2.24% |
TTCT | 2.23% |
TCCC | 2.17% |