Input data and parameters
Input
Analysis date: | Tue Oct 31 09:31:49 GMT 2023 |
BAM file: | SRX7354329.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): | 31,873,611 / 31,832,867 |
Number of aligned pairs (without duplicates): | 31,828,146 |
Total number of alignments: | 67,833,400 |
Number of secondary alignments: | 4,126,922 |
Number of non-unique alignments: | 6,949,009 |
Aligned to genes: | 53,035,953 |
Ambiguous alignments: | 164,404 |
No feature assigned: | 7,415,634 |
Missing chromosome in annotation: | 268,400 |
Not aligned: | 14,819,606 |
Reads genomic origin
Exonic: | 53,035,953 / 87.73% |
Intronic: | 4,349,125 / 7.19% |
Intergenic: | 3,066,509 / 5.07% |
Intronic/intergenic overlapping exon: | 1,909,839 / 3.16% |
Transcript coverage profile
5' bias: | 0.36 |
3' bias: | 0.16 |
5'-3' bias: | 2.4 |
Junction analysis
Reads at junctions: | 16,301,757 |
ACCT | 5.32% |
AGGT | 4.78% |
ATCT | 3.79% |
AGGA | 3.68% |
TCCT | 3.41% |
GCCT | 2.97% |
AGCT | 2.71% |
CCCT | 2.45% |
AGGC | 2.4% |
AGAT | 2.35% |
TTCT | 2.22% |