Input data and parameters
Input
Analysis date: | Sun Oct 29 01:57:44 GMT 2023 |
BAM file: | SRX7354099.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): | 32,739,446 / 32,707,132 |
Number of aligned pairs (without duplicates): | 32,701,198 |
Total number of alignments: | 69,858,176 |
Number of secondary alignments: | 4,411,598 |
Number of non-unique alignments: | 6,989,813 |
Aligned to genes: | 56,402,585 |
Ambiguous alignments: | 215,522 |
No feature assigned: | 5,862,154 |
Missing chromosome in annotation: | 388,102 |
Not aligned: | 4,158,452 |
Reads genomic origin
Exonic: | 56,402,585 / 90.59% |
Intronic: | 3,593,741 / 5.77% |
Intergenic: | 2,268,413 / 3.64% |
Intronic/intergenic overlapping exon: | 2,195,794 / 3.53% |
Transcript coverage profile
5' bias: | 0.13 |
3' bias: | 0.16 |
5'-3' bias: | 2.05 |
Junction analysis
Reads at junctions: | 17,886,348 |
ATCT | 5.08% |
ACCT | 4.81% |
TCCT | 4.62% |
AGGT | 4.48% |
CCCT | 3.55% |
AGGA | 3.04% |
GCCT | 2.62% |
TTCT | 2.42% |
AGCT | 2.12% |
AGGC | 2.08% |
AGAA | 1.96% |