Input data and parameters
Input
Analysis date: | Sun Oct 29 01:33:19 GMT 2023 |
BAM file: | SRX7354135.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): | 32,907,421 / 32,881,427 |
Number of aligned pairs (without duplicates): | 32,877,541 |
Total number of alignments: | 69,879,120 |
Number of secondary alignments: | 4,090,272 |
Number of non-unique alignments: | 6,767,039 |
Aligned to genes: | 54,390,617 |
Ambiguous alignments: | 186,582 |
No feature assigned: | 8,221,258 |
Missing chromosome in annotation: | 313,624 |
Not aligned: | 5,995,000 |
Reads genomic origin
Exonic: | 54,390,617 / 86.87% |
Intronic: | 5,504,175 / 8.79% |
Intergenic: | 2,717,083 / 4.34% |
Intronic/intergenic overlapping exon: | 2,218,566 / 3.54% |
Transcript coverage profile
5' bias: | 0.34 |
3' bias: | 0.2 |
5'-3' bias: | 1.89 |
Junction analysis
Reads at junctions: | 17,881,100 |
ACCT | 5.33% |
AGGT | 4.74% |
ATCT | 3.62% |
AGGA | 3.58% |
TCCT | 3.55% |
GCCT | 3.2% |
AGCT | 2.73% |
CCCT | 2.52% |
AGGC | 2.38% |
AGAT | 2.28% |
TTCT | 2.1% |