Pre-made Library Sequencing QC Analysis Report


Contract IDH204SC24073125
Contract NameNVUK2024062819-NL_Radboud_scRNA and scATAC_WOBI_Yutaka
Batch IDX204SC24073125-Z02-F001
Report Time20240806
ReminderPartial results are presented in this report, while full results will be delivered in data release.


Novogene Co., Ltd


1 Introduction

From the pre-made libraries receiving to the final data, each step will influence the final analysis results. To guarantee the reliability of results, Novogene will perform the quality control on each step of the procedure. Workflow is shown as follows:

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2 Results and Instructions

The ASCII value of each character at the fourth line minus 33 equals to the Phred-scaled quality value of the corresponding sequenced base in the second line. The relationship between sequencing error rate (e) and base quality value (Qphred) can be expressed by the following equation:

Qphred = -10log10(e)

The correlations between sequencing error rate and sequencing quality are available on illumina's official website.

Novogene Co., Ltd


3 Summary of Sequencing Data Information

The total output of data on the sequencer: Raw data 1170.06 G.

The raw data and sequencing quality are shown in Table 1.

Table 1 Data Quality Summary

SampleLibraryFlowcell_LaneRaw readsRaw data(G)Q30(%)
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005280-1a22MF3CLT3_L11505170000146.6766.62
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005281-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005279-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005285-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005281-1a22MF3CLT3_L21507510000147.7866.35
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005285-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005279-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005280-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005285-1a22MF3CLT3_L31485070000145.5965.10
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005280-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005281-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005279-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005279-1a22MF3CLT3_L41492060000146.1565.52
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005281-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005280-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005285-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005284-1a22MF3CLT3_L51491570000146.1868.32
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005286-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005282-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005283-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005283-1a22MF3CLT3_L61493480000146.2068.33
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005282-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005286-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005284-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005282-1a22MF3CLT3_L71486500000145.5667.95
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005284-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005286-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005283-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005283-1a22MF3CLT3_L81492980000145.9368.26
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005282-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005286-1a
sublibrary1,sublibrary2,sublibrary3,sublibrary4MKDL240005284-1a

    (1) Sample: Sample ID.
    (2) Library: Library ID.
    (3) Flowcell_Lane:Flowcell ID_lane ID.
    (4) Raw reads: The number of sequencing reads pairs; four lines would be considered as one unit according to the format of FASTQ.
    (5) Raw data: The original sequencing data.
    (6) Q30: The percent of bases with phred-scaled quality scores greater than 30.

Novogene Co., Ltd


4 Appendix

4.1 BCL Format

BCL files with binary format are the raw data files of the illumina sequencing run. The BCL file contains the base call and associated quality score for every cluster of each sequencing cycle. To convert BCL format to FASTQ format, the illumina-developed or the third party demultiplexing tools, bcl2fastq or cellranger for 10x single cell RNA sequencing, etc., need to be applied.. Novogene delivers the following files which are required for demultiplexing.

  1. .cbcl
  2. RunCompletionStatus.xml
  3. RunInfo.xml
  4. RunParameters.xm

4.2 References

Hansen K.D. et al (2010). Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic acids research 38, e131-e131.

Erlich Y.et al (2008). Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.Nature Methods,5,679-682.

Jiang L.C. et al (2011). Synthetic spike-in standards for RNA-seq experiments. Genome research 21, 1543-1551.