Input data and parameters
Input
Analysis date: | Mon Oct 30 20:09:40 GMT 2023 |
BAM file: | SRX7354198.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): | 38,215,094 / 38,192,852 |
Number of aligned pairs (without duplicates): | 38,190,131 |
Total number of alignments: | 81,210,745 |
Number of secondary alignments: | 4,802,799 |
Number of non-unique alignments: | 8,040,508 |
Aligned to genes: | 64,526,635 |
Ambiguous alignments: | 215,579 |
No feature assigned: | 8,087,077 |
Missing chromosome in annotation: | 340,946 |
Not aligned: | 3,218,298 |
Reads genomic origin
Exonic: | 64,526,635 / 88.86% |
Intronic: | 5,282,114 / 7.27% |
Intergenic: | 2,804,963 / 3.86% |
Intronic/intergenic overlapping exon: | 2,364,879 / 3.26% |
Transcript coverage profile
5' bias: | 0.35 |
3' bias: | 0.2 |
5'-3' bias: | 2.12 |
Junction analysis
Reads at junctions: | 20,443,792 |
ACCT | 5.45% |
AGGT | 4.57% |
ATCT | 3.8% |
TCCT | 3.46% |
AGGA | 3.37% |
GCCT | 3.25% |
AGCT | 2.72% |
TTCT | 2.47% |
CCCT | 2.43% |
AGGC | 2.3% |
AGAT | 2.19% |