Report

Name of the analysis run report

Status

Status of the analysis (e.g., Started, Complete)

Flows

Number of flow cycles from the actual sequencing run

TF Name*

Test Fragment Name

Q10 Mean*

Average Q10 read length.

Q17 Mean*

Average Q17 read length

System SNR*

System Signal-to-Noise Ratio

50Q10 Reads*

Number of TF Ion Sphere Particles (ISP) at 50+ bp at Q10

50Q17 Reads*

Number of TF Ion Sphere Particles (ISP) at 50+ bp at Q17

Keypass Reads*

Number of reads that have test fragment keys

TF Key Peak Counts*

Signal strength of the first three bases of the TF key

Total_Num_Reads

Total number of reads

Library_50Q10_Reads

Reads of length at least 50bp with 90% or greater accuracy

Library_100Q10_Reads

Reads of length at least 100bp with 90% or greater accuracy

Library_200Q10_Reads

Reads of length at least 200bp with 90% or greater accuracy

Library_Mean_Q10_Length

Average length of reads with 90% or greater accuracy

Library_Q10_Coverage

Average per base coverage considering reads with 90% or greater accuracy

Library_Q10_Longest_Alignment

Longest read length amongst reads with 90% or greater accuracy

Library_Q10_Mapped Bases

Total bases from reads with 90% or greater accuracy

Library_Q10_Alignments

Number of alignments from reads with 90% or greater accuracy

Library_50Q17_Reads

Reads of length at least 50bp with 98% or greater accuracy

Library_100Q17_Reads

Reads of length at least 100bp with 98% or greater accuracy

Library_200Q17_Reads

Reads of length at least 200bp with 98% or greater accuracy

Library_Mean_Q17_Length

Average length of reads with 98% or greater accuracy

Library_Q17_Coverage

Average per base coverage considering reads with 98% or greater accuracy

Library_Q17_Longest_Alignment

Longest read length amongst reads with 98% or greater accuracy

Library_Q17_Mapped Bases

Total bases from reads with 98% or greater accuracy

Library_Q17_Alignments

Number of alignments from reads with 98% or greater accuracy

Library_50Q20_Reads

Reads of length at least 50bp with 99% or greater accuracy

Library_100Q20_Reads

Reads of length at least 100bp with 99% or greater accuracy

Library_200Q20_Reads

Reads of length at least 200bp with 99% or greater accuracy

Library_Mean_Q20_Length

Average length of reads with 99% or greater accuracy

Library_Q20_Coverage

Average per base coverage considering reads with 99% or greater accuracy

Library_Q20_Longest_Alignment

Longest read length amongst reads with 99% or greater accuracy

Library_Q20_Mapped_Bases

Total bases from reads with 99% or greater accuracy

Library_Q20_Alignments

Number of alignments from reads with 99% or greater accuracy

Library_Key_Peak_Counts

Signal strength of the first three bases of the library key

Library_50Q47_Reads

Number of perfect reads of length at least 50bp

Library_100Q47_Reads

Number of perfect reads of length at least 100bp

Library_200Q47_Reads

Number of perfect reads of length at least 200bp

Library_Mean_Q47_Length

Average length of perfect reads

Library_Q47_Coverage

Average per base coverage considering only perfect reads

Library_Q47_Longest_Alignment

Longest reads length amongst perfect reads

Library_Q47_Mapped_Bases

Total bases from perfect reads

Library_Q47_Alignments

Number of alignments from perfect reads

Library_CF

CAFIE metric: Carry forward

Library_IE

CAFIE metric: Incomplete extension

Library_DR

CAFIE metric: Signal/polymerase loss (droop)

Library_SNR

System Signal-to-Noise Ratio

Sample

Name of the sample

Library

Name of the reference genome

Notes

Any additional user-provided notes

Run Name

Long name of the analysis run

PGM Name

Name of the Ion S5, PGM, or Proton instrument where the sample was sequenced

Run Date

Date the sample was sequenced

Run Directory

Location of the raw DAT files on the Torrent Server

Num_Washouts

NA

Num_Dud_Washouts

NA

Num_Washout_Ambigous

NA

Num_Washout_Live

NA

Num_Washout_Test_Fragment

NA

Num_Washout_Library

NA

Library_Pass_Basecalling

NA

Library_pass_Cafie

NA

Number_Ambiguous

NA

Number_Live

Number of wells producing a signal

Number_Dud

Number of wells with ISPs but no signal

Number_TF

Number of wells containing test fragment

Number_Lib

Number of wells containing library

Number_Bead

Number of wells containing beads

Library_Live

Number of wells containing library ISP with signal

Library_Keypass

Number of wells containing library ISP with signal and match key

TF_Live

Number of wells containing test fragment ISP with signal

TF_Keypass

Number of wells containing test fragment ISP with signal and match key

Keypass_All_Beads

Number of wells containing ISP with signal and match key

P

JSON string of plugin data

s

JSON string of plugin data