针对老师们问到的三代数据分析中的一些问题，今天主要针对基本信息分析中的测序数据统计、质量QC评估，data summary等，结合项目案例解释如下：

General - Filtering Report

* Polymerase Read Bases : The number of bases in the polymerase read.

即测序获得所有数据量，包含adaptors序列。

* Polymerase Reads : The number of polymerases generating high quality reads. Polymerase reads are trimmed to the high quality region and include bases from adaptors, as well as potentially multiple passes around a circular template.

即高质量测序reads，包含adaptors以及测多次获得multiple subreads。

* Polymerase Read N50 : 50% of all polymerase reads are longer than this value.

测序reads中，50%的reads长度大于N50这个值。

* Polymerase Read Length : The mean trimmed read length of all polymerase reads. The value includes bases from adaptors as well as multiple passes around a circular template.

测序reads的平均长度，包含adaptors以及multiple subreads。

* Polymerase Read Quality : The mean single-pass read quality of all polymerase reads.

测序reads中，single-pass read平均质量值。

* Post-Filter Polymerase Read Bases : The number of bases in the polymerase reads after filtering, including adaptors.

测序reads过滤后所包含的碱基数，包含adaptors以及multiple subreads。

* Post-Filter Polymerase Reads : The number of polymerases generating trimmed reads after filtering. Polymerase reads include bases from adaptors and multiple passes around a circular template.

过滤后测序reads数，过滤后reads中包含adaptors以及multiple subreads。

* Post-Filter Polymerase Read Length : The mean trimmed read length of all polymerase reads after filtering. The value includes bases from adaptors as well as multiple passes around a circular template.

过滤后测序reads的平均长度，过滤后reads中包含adaptors以及multiple subreads。

* Post-Filter Polymerase Read Quality : The mean single-pass read quality of all polymerase reads after filtering.

过滤后测序reads中，single-pass read平均质量值。

附其他输出报告中的名词释义：

Diagnostic - Adapters Report

• Adapter Dimers (%): The % of pre-filter ZMWs which have observed inserts of 0-10bp. These are likely adapter dimers.

  接头二聚体(%): 测序reads过滤前，其中0-10bp的序列，极有可能为接头二聚体。

• Short Inserts (%): The % of pre-filter ZMWs which have observed inserts of 11-100bp. These are likely short fragment contamination.

  短的插入片段(%): 测序reads过滤前，其中11-100bp的序列，极有可能为短的污染序列。
  

Diagnostic - Spike-In Control Report

• Control Sequence: The name of the control sequence.

  对照序列/样本的信息。
  

• Control Reads (%): The percent of post-filter polymerase reads that are from the control sample. The formula for this is: (total # of control reads)/(total # of post-filter reads).

  测序reads过滤后，control reads所占过滤后reads的比例。计算公式为： (total # of control reads)/(total # of post-filter reads).
  

• Control Polymerase Read Length: The mean mapped read length of the polymerase reads from the control sample.

  对照样品测序reads中，可比对上的reads的平均长度。
  

• Control Reads: The total number of polymerase reads from the control sample that passed filtering.

  经过滤后，对照样本中总的测序reads数。
  

• Control Subread Accuracy: The mean single-pass accuracy of the mapped polymerase reads from the control sample.

  对照样本中，可比对上的测序reads的平均single-pass准确性。
  

• Control Polymerase Read Length 95%: The 95th percentile of mapped read length of the polymerase reads from the control sample.

  对照样本中，比对率在95%的reads长度。
  

Diagnostic - Loading Report

• SMRT Cell ID: ID number of the SMRT Cell(s) used in this run.

  此次运行中，SMRT Cell(s)的ID号。
  

• Productive ZMWs: The number of ZMWs for this SMRT Cell that produced results with Productivity = 1.

  此测序SMRT cell中，零膜波导孔测序产生的序列结果，且聚合酶填充率Productivity = 1。
  

• Productivity 0 (%): Percentage of ZMWs that are empty, with no polymerase.

  零膜波导孔没有被聚合酶填充，是空的。
  

• Productivity 1 (%): Percentage of ZMWs that are productive and sequencing.

  零膜波导孔被聚合酶填充满，可开展测序。
  

• Productivity 2 (%): Percentage of ZMWs that are not P0 (empty) or P1 (productive). This may occur for a variety of reasons and the sequence data is not usable.

  零膜波导孔填充值既不是P0 (empty) 也不是 P1 (productive)。这可能是由多方面的原因导致的、且测序数据不可用。
  

Resequencing - Coverage Report

• Coverage: The mean depth of coverage across the reference sequence.

  总测序数据量相对参考基因组序列的平均覆盖度（平均测序深度）。
  

• Missing Bases (%): The percentage of the reference sequence that has zero coverage.

  参考基因组序列中完全没有被覆盖到的区域，即该区域测序深度为0。
  

Resequencing - Mapping Report

• Post-Filter Reads: The number of reads that passed filtering.

  过滤后的reads数。
  

• Mapped Reads: The number of post-filter reads that mapped to the reference sequence.

  过滤后的reads中，可比对至参考基因组序列上的reads数。
  

• Mapped Subreads: The number of post-filter subreads that mapped to the reference sequence.

  过滤后获得的subreads中，可比对至参考基因组序列上的subreads数。
  

• Mapped CCS Reads: The number of post-filter CCS reads that mapped to the reference sequence.

  CCS即为consensus sequence，由来自同一个ZMWs的subreads比对获得。

  这里是指过滤后，可比对至参考基因组序列上的CCS序列数。

• Mapped Subread Bases: The number of post-filter bases from all subreads that mapped to the reference sequence. This does not include adapters.

  过滤后，可比对至参考基因组序列上的subreads的总碱基数。这里不包含adapters。
  

• Mapped CCS Read Bases: The number of post-filter CCS read bases that mapped to the reference sequence. This does not include adapters.

  过滤后，可比对至参考基因组序列上的CCS的总碱基数。这里不包含adapters。
  

• Mapped Subread Accuracy: The mean accuracy of post-filter subreads that mapped to the reference sequence.

  过滤后，可比对至参考基因组序列上的subreads的平均准确性。
  

• Mapped CCS Read Accuracy: The mean accuracy of post-filter CCS reads that mapped to the reference sequence.

  过滤后，可比对至参考基因组序列上的CCS的平均准确性。
  

• Mapped Subread Length: The mean read length of post-filter subreads that mapped to the reference sequence. This does not include adapters.

  过滤后，可比对至参考基因组序列上的subreads的平均长度。这里不包含adapters。
  

• Mapped Read Length of Insert: The mean read length of all insert sequences, which includes only mapped sequences. The read length of insert is approximately the longest subread length per ZMW.

  过滤后，可比对至参考基因组序列上的所有插入片段的平均长度。在同一个ZMW中，插入片段的长度大约是该ZMW中最长的subread的长度。
  

• Mapped Polymerase Read Length: The mean read length of post-filter polymerase reads that mapped to the reference sequence. This includes adapters.

  过滤后，可比对至参考基因组序列上的测序reads的长度，Polymerase Read是包含adapters的。
  

• Mapped Polymerase Read Length 95%: The 95th percentile of read length of post-filter polymerase reads that mapped to the reference sequence.

  过滤后，可比对至参考基因组序列上，比对率在95%的polymerase reads的长度。
  

• Mapped Polymerase Read Length Max: The maximum read length of post-filter polymerase reads that mapped to the reference sequence.

  过滤后，可比对至参考基因组序列上的最长的polymerase reads的长度。
  

• Mapped Full Subread Length: The average of the lengths of full subreads that mapped to the reference sequence. Full subreads are subreads flanked by two adapters.

  过滤后，可比对至参考基因组序列上的full subreads的平均长度。full subreads两侧均包含adapter。
  

Analysis - Variants Report

• Reference: The name of the reference sequence.

• Reference Length: The length of the reference sequence.

• Bases Called (%): The percentage of reference sequence that has ≥ 1x coverage. % Bases Called + % Missing Bases should equal 100.

• Consensus Accuracy: The accuracy of the consensus sequence compared to the reference.

• Base Coverage: The mean depth of coverage across the reference sequence.

Analysis - Top Variants Report

• Sequence: The name of the reference sequence.

• Position: The position of the variant along the reference sequence.

• Variant: The variant position, type, and affected nucleotide.

• Type: The variant type: Insertion, Deletion, or Substitution.

• Coverage: The coverage at position.

• Confidence: The confidence of the variant call.

• Genotype: Includes the full number of chromosomes (diploid) or half the number (haploid).

Assembly - Iterations Report

• Assembly Iterations: The number of iterations of overlap-layout-consensus performed by the de novo or hybrid assembly algorithm.

Assembly - Draft Assembly Report

• Draft Contigs: The number of contigs output by Celera Assembler, which may include singleton and degenerate contigs. After assembly polishing with Quiver, the final number of contigs may be smaller.

• N50 Contig Length: The length L of the contig for which 50% of all bases in the final contigs are of length greater than L.

• Reads Assembled (%): The fraction of all reads that are assembled into contigs in the final assembly.

• Max Contig Length: The length of the longest contig in the final assembly.

• Sum of Contig Lengths: The sum of the lengths of all contigs in the final assembly.

Hybrid Assembly - Assembly Iterations Report

• Input Contigs: The number of contigs used as input to the AHA algorithm.

• Min Align Score: The minimum alignment score between a read and a contig to use the alignment for scaffolding.

• Min Link Redundancy: The minimum number of reads that must link two contigs for those contigs to be connected in a scaffold.

• Min Subread Length: The minimum length required for a subread to be used by the AHA algorithm.

• Min Contig Length: The minimum length required for a contig to be used by the AHA algorithm.

• Scaffolds Across Assembly Iterations: The number of scaffolds at a particular iteration of the AHA algorithm.

• Linking Reads Across Assembly Iterations: The number of linking reads at a particular iteration of the AHA algorithm.

Hybrid Assembly - Final Assembly Report

• Number: The number of scaffolds, contigs, or gaps in the initial or final assembly.

• Max Length: The length of the longest scaffold, contig, or gap in the initial or final assembly.

• N50 Length: The length L of the scaffold, contig, or gap for which 50% of all bases in the initial/final scaffold/contig/gap are of length greater than L.

• Sum Length: The sum of the lengths of all scaffolds, contigs, or gaps in the initial or final assembly.

• Initial Scaffolds: The distribution of the lengths of the scaffolds sequences before completing the AHA algorithm. Scaffolds are composed of contigs optionally separated by gap sequences.

• Final Scaffolds: The distribution of the lengths of the scaffolds sequences after completing the AHA algorithm. Scaffolds are composed of contigs optionally separated by gap sequences.

• Initial Contigs: The distribution of the lengths of the contig sequences before completing the AHA algorithm. Contigs are stretches of continuous sequence that do not contain gaps.

• Final Contigs: The distribution of the lengths of the contig sequences after completing the AHA algorithm. Contigs are stretches of continuous sequence that do not contain gaps.

• Initial Gaps: The distribution of the lengths of the gaps between contig sequences before completing the AHA algorithm.

• Final Gaps: The distribution of the lengths of the gaps between contig sequences after completing the AHA algorithm.

Base Modifications - Motifs Report

• Motif: The nucleotide sequence of the methyltransferase recognition motif, using the standard IUPAC nucleotide alphabet.

• Modified Position: The position within the motif that is modified. The first base is "1". Example: The modified adenine in GATC is at position 2.

• Modification Type: The type of chemical modification most commonly identified at that motif. These are: 6mA, 4mC, 5mC, or modified_base (modification not recognized by the software.)

• % Motifs Detected: The percentage of times that this motif was detected as modified across the entire genome.

• # Of Motifs Detected: The number of times that this motif was detected as modified across the entire genome.

• # Of Motifs In Genome: The number of times this motif occurs in the genome.

• Mean Modification QV: The mean modification QV for all instances where this motif was detected as modified.

• Mean Motif Coverage: The mean coverage for all instances where this motif was detected as modified.

• Partner Motif: For motifs that are not self-palindromic, this is the complementary sequence.

Assembly - Pre-Assembly Report

• Seed Bases: The number of bases from seed reads.

• Pre-Assembled Yield: The percentage of seed read bases that were successfully aligned to generate pre-assembled reads.

• Pre-Assembled Read Length: The average length of the pre-assembled reads.

• Length Cutoff: Reads with lengths greater than the length cutoff are used as seed reads for pre-assembly.

• Pre-Assembled Bases: The number of bases in the pre-assembled reads.

• Pre-Assembled Reads: The number of reads output by the pre-assembler. Pre-assembled reads are very long, highly accurate reads that can be used as input to a de novo assembler.

• Pre-Assembled N50: The N50 read length of the pre-assembled reads.

待继续更新。