SEQdata-BEACON

The detailed description of the metrics

Index Name Description
1CycleNumberTotal sequencing cycle number. One sequencing cycle equals to one base in sequencing read length.
2TypeSequencing type and read length.
3ChipThe position of chip on the sequencer, normally it is distinguished by A/B.
4Reads(M)The number of DNBs recognized by the Basecall software.
5R1ReadNumThe number of DNBs recognized by the Basecall software in Read 1.
6R2ReadNumThe number of DNBs recognized by the Basecall software in Read 2.
7Base(G)The number of bases recognized by the Basecall software.
8R1BaseNumThe number of bases recognized by the Basecall software in Read 1.
9R2BaseNumThe number of bases recognized by the Basecall software in Read 2.
10FITFIT value represents the distribution of differences between signal and noise for each base. The FIT value is higher when the distribution of differences between signal to noise for each channel/color are more concentrated.
11InitialFIT%The average FIT value of the first sequencing cycle.
12ForFIT(5_35)%Average FIT value of sequencing cycle 35 of Read1/ average FIT value of sequencing cycle 5 of Read1*100%.
13RevFIT(5_35)%Average FIT value of sequencing cycle 35 of Read2/ average FIT value of sequencing cycle 5 of Read2*100%.
14ESR%Effective Spot Rate,the percentage of filtered Reads among the DNBs recognized by Basecalling. ESR = (Total Reads/theoretical maximum reads number of one sequencing lane) ×100%.
15StartEsr%Start Effective Spot Rate,it is the intermediate value of totalESR when the sequencing begins.
16TotalEsr%TotalEsr calculated ESR value in the first 15 cycles in read1 and read2, and kept constant in the rest of each read.
17ChipProductivity%Flow cell chip productivity, ChipProductivity%= Effective FOVs (Field Of View)*ESR (Effective Spot Rate)/Total FOVs (Field Of View).
18DnbnumberThe theoretical maximum number of DNBs on the patterned array.
19SNRSignal to Noise Ratio, taking the SNR calculation of a single DNB as an example, while A base (maximum light intensity) is used as the signal, the CGT is the background, and the variance of the CGT light intensity is noise. A_SNR=A_mean/CGT_dev.
20BICBasecall information content, the percentage of DNBs that can be used for Basecalling among the DNBs recognized by the optical system. BIC = (numbers of DNB that can be used for Basecalling/numbers of DNB that can be recognized by the optical systems) ×100%.
21accGRRAccumulated Good Reads Rate, taking chastity greater than 0.6 as the filtering criteria, the percentage of filtered Reads among the DNBs recognized by Basecalling. accGRR = Total Reads/theoretical maximum reads number of one sequencing lane. This value is only a statistical indicator which reflects the overall quality of the read (multi-cycle state).
22IntensityLight intensity of each base ATCG for each cycle.
23Q30%The percentage of bases with an error rate below 0.001 (accuracy above 99.9%).
24R1Q30%The percentage of bases with an error rate below 0.001 (accuracy above 99.9%) in Read 1.
25R2Q30%The percentage of bases with an error rate below 0.001 (accuracy above 99.9%) in Read 2.
26R1Q20%The percentage of bases with an error rate below 0.01 (accuracy above 99%) in Read 1.
27R2Q20%The percentage of bases with an error rate below 0.01 (accuracy above 99%) in Read 2.
28totalEstErr%Estimated error rate, which means, for each cycle base, estimating the average error rate for each cycle based on the Phred score calculation formula and the current quality value. TotalEstErr% means EstErr value in the sequencing lane.
29R1EstErr%R1EstErr% means EstErr value in Read 1.
30R2EstErr%R2EstErr% means EstErr value in Read 2.
31totalCG%(Total count of G bases + Total count of C bases)/total base number in this sequencing lane*100%
32R1CG%(Total count of G bases in Read 1+ Total count of C bases in Read 1)/total base number in Read 1*100%
33R2CG%(Total count of G bases in Read 2+ Total count of C bases in Read 2)/total base number in Read 2*100%
34RecoverValue(A)Signal recovery rate of A bases in paired-end second strand sequencing, which is used for intensity calibration.
35RecoverValue(C)Signal recovery rate of C bases in paired-end second strand sequencing, which is used for intensity calibration.
36RecoverValue(G)Signal recovery rate of G bases in paired-end second strand sequencing, which is used for intensity calibration.
37RecoverValue(T)Signal recovery rate of T bases in paired-end second strand sequencing, which is used for intensity calibration.
38RecoverValue(AVG)Signal recovery rate of ATCG bases in paired-end second strand sequencing, which is used for intensity calibration.
39baseTypeDistAThe percentage of A bases in each cycle. baseTypeDistA = Total count of A bases/total base number in this sequencing lane*100%.
40baseTypeDistCThe percentage of C bases in each cycle. baseTypeDistC = Total count of C bases/total base number in this sequencing lane*100%.
41baseTypeDistTThe percentage of T bases in each cycle. baseTypeDistT = Total count of T bases/total base number in this sequencing lane*100%.
42baseTypeDistGThe percentage of G bases in each cycle. baseTypeDistG = Total count of G bases/total base number in this sequencing lane*100%.
43baseTypeDistNThe percentage of N bases in each cycle. baseTypeDistN = Total count of N bases/total base number in this sequencing lane*100%.
44LagDuring the sequencing reaction, theoretically the read DNA strands on a DNB extends by one base per cycle. Lag and Runon record the read strands being out of phase with the current cycle. Lag indicates one base short.
45Lag1%The percentage of Lag bases in Read 1.
46Lag2%The percentage of Lag bases in Read 2.
47RunonDuring the sequencing reaction, theoretically the read DNA strands on a DNB extends by one base per cycle. Lag and Runon record the read strands being out of phase with the current cycle. Runon indicates one base ahead.
48Runon1%The percentage of Runon bases in Read 1.
49Runon2%The percentage of Runon bases in Read 2.
50SplitRate%Barcode split rate, the ratio of reads split by #1-96 barcode to all sequenced reads.
51MAXOffsetXThe offset values in the X and Y directions of each cycle of each FOV with regards to the first cycle. For each cycle, the average of offsets of all FOVs represent the offset value of this cycle. MaxOffsetX metric tells the largest average offset of all FOVs in all sequencing cycles in X axis.
52MAXOffsetYThe offset values in the X and Y directions of each cycle of each FOV with regards to the first cycle. For each cycle, the average of offsets of all FOVs represent the offset value of this cycle. MaxOffsetY metric tells the largest average offset of all FOVs in all sequencing cycles in Y axis.
53InitialOffsetXThe average offset of all FOVs in A channel in the first cycle in the X directions with regards to the flow cell template design.
54InitialOffsetYThe average offset of all FOVs in A channel in the first cycle in the Y directions with regards to the flow cell template design.
55ThetaThe angle between the moving direction of the array stage and the track line on the array.
56InitialSignalThe average signal intensity of the first cycle in the sequencing lane.
57ForSignal(5_35)%Average signal intensity of sequencing cycle 35 of Read1/ average signal intensity of sequencing cycle 5 of Read1*100%.
58RevSignal(5_35)%Average signal intensity of sequencing cycle 35 of Read2/ average signal intensity of sequencing cycle 5 of Read2*100%.
59ImageAreaNumber of FOV (Field Of View) imaged in this specific sequencing run.
60FCUnique code of sequencing chips which encrypted by MD5 for protecting the commercial samples information.
61Reagent ID(4)The lot number of 4 ℃ reagent.
62Reagent ID(-20)The lot number of -20 ℃ reagent.
63FClotThe lot number of flow cell.
64StarttimeThe sequencing start time.
65ResultsThe identification and documentation the status of sequencing completion.