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Understanding Quality Classes Draft 'B' Revision 1.1 What are Quality Classes? A Quality Class is a single number representation of a set of quality attributes. They range in value from 0 to 23, and take into account attributes regarding the quality value, direction, and agreement of the bases in a slice. Typically, slices with quality classes from 1 to 8 are considered high quality, and 9 through 23 are considered low quality. However, the classes do not follow a strict ranking overall, so a class may or may not be of lower quality (by some other measure) than the preceding class. Low quality slices are typically candidates for resequencing or editing. Quality class 0 is used to indicate that the slice is in error, or that there was an internal error in the calculation. Quality Class Quick Reference Guide. Definitions Slice A slice is a one base wide cut of an assembly. It is composed of 0 or more reads stacked vertically at an offset in the assembly. Each read contributes a base with a quality value and a direction (either forward or reverse). A slice also has a consensus, which represents the most likely base represented by the slice. High/Low Quality Base A base is considered to be of high quality if its quality value is greater than or equal to a high quality threshold. Bases that do not reach the threshold are considered low quality. The threshold can be set as a parameter of the calculation, but 30 is used by default. The terms high and low quality reads refer to the reads which contribute the high or low quality bases respectively. High/Low Quality Conflict A slice is said to have a high quality conflict if there is at least one base in the slice that has high quality that does not match the consensus. A low quality conflict means that there is at least one low quality base that does not match the consensus. Quality Class Attributes Note: For the purposes of agreement, ambiguity codes are not resolved into the component reads, i.e. M and A are in conflict. Conflict Attributes ATTR_No_Conflict Indicates all of the bases in the slice are in agreement with the consensus. ATTR_Non_Quality_Conflict Indicates there is at least one low quality base that conflicts with the consensus. ATTR_Quality_Conflict Indicates there is at least one high quality base that conflicts with the consensus. Note: ATTR_No_Conflict, ATTR_Quality_Conflict, and ATTR_Non_Quality_Conflict are mutually exclusive and exhaustive for represening if the bases in a slice are in agreement with the consensus. Quality Attributes ATTR_Quality_Strand Indicates there is at least one high quality base in at least one direction which agrees with the consensus. ATTR_Non_Quality_Strand Indicates there are no high quality bases in either direction that agree with the consensus, but there is at least one low quality base that does agree in at least one direction. ATTR_Quality_Same_Strand Indicates there are at least two high quality bases in the same direction agreeing with the consensus in at least one direction. Implies ATTR_Quality_Strand ATTR_Non_Quality_Same_Strand Indicates there is at least two bases in the same direction agreeing with the consensus, but at most one high quality base in that direction. Implies ATTR_Quality_Strand or ATTR_Non_Quality_Strand ATTR_Any_Same_Strand Indicates either ATTR_Non_Quality_Same_Strand or ATTR_Quality_Same_Strand. ATTR_Quality_Other_Strand Indicates there is at least one high quality base in both directions which agree with the consensus. Implies ATTR_Quality_Strand ATTR_Non_Quality_Other_Strand Indicates there is at least one low quality base in both directions which agree with the consensus. Implies either ATTR_Quality_Strand or ATTR_Non_Quality_Strand ATTR_Single_Coverage Indicates that there is only one base that agrees with the consensus. Consensus Attributes ATTR_Ambiguity Indicates that the consensus is ambiguous, i.e. not one of {A,C,G,T,-}. ATTR_GAP_Consensus Indicates that the consensus is a gap. Other Attributes ATTR_Zero_Coverage Indicates that the depth of coverage is zero, there are no underlying sequences in the slice at the current contig position. Quality Classes Definitions Once all of the attributes have been calculated, a quality class is choosen to represent the set of attributes present in the slice. Here each class is described and the attributes that it represents are listed and an example slice of that quality class. A slice takes the lowest numbered (highest quality) class that matches the slice in the case where a slice matches more than one class. Note: "In agreement" means the base is in agreement with the consensus. Quality Class 0 A quality class of 0 is used to indicate that there are no reads in the slice, and there is a zero depth of coverage. Note: Quality Class 0 is also used to indicate that there was an internal error while calculating quality classes. Please report all slices that do not have gap as consensus and have quality class 0 to bits.closure. ATTR_Zero_Coverage Consensus: - () Quality Class 1 No conflict, and at least one high quality base in both directions in agreement. ATTR_No_Conflict ATTR_Quality_Other_Strand Consensus: A (A, 30, Forward) (A, 30, Reverse) Quality Class 2 No conflict, and at least one high quality base in one direction in agreement, and at least one low quality base in the other direction in agreement. ATTR_No_Conflict ATTR_Quality_Strand ATTR_Non_Quality_Other_Strand Consensus: A (A, 30, Forward) (A, 20, Reverse) Quality Class 3 No conflict, and at least one high quality base in agreement, and at least one other base in agreement in that same direction. ATTR_No_Conflict ATTR_Quality_Strand ATTR_Any_Same_Strand Consensus: A (A, 30, Forward) (A, 20, Forward) Quality Class 4 No conflict, and at least one low quality base in both directions in agreement. ATTR_No_Conflict ATTR_Non_Quality_Other_Strand Consensus: A (A, 20, Forward) (A, 20, Reverse) Quality Class 5 No conflict, and at least two low quality bases in a single direction in agreement. ATTR_No_Conflict ATTR_Non_Quality_Same_Strand Consensus: A (A, 20, Forward) (A, 20, Forward) Quality Class 6 Low quality conflict, and at least one high quality base in both directions in agreement. ATTR_Non_Quality_Conflict ATTR_Quality_Other_Strand Consensus: A (A, 30, Forward) (A, 30, Reverse) (T, 20, Reverse) Quality Class 7 Low quality conflict, and at least one high quality base in one direction in agreement, and at least one low quality base in the other direction in agreement. ATTR_Non_Quality_Conflict ATTR_Quality_Strand ATTR_Non_Quality_Other_Strand Consensus: A (A, 30, Forward) (A, 20, Reverse) (T, 20, Reverse) Quality Class 8 Low quality conflict, and at least one high quality base in one direction in agreement, and at least one other base also in that direction in agreement. ATTR_Non_Quality_Conflict ATTR_Quality_Strand ATTR_Any_Same_Strand Consensus: A (A, 30, Forward) (A, 20, Forward) (T, 20, Reverse) Quality Class 9 No conflict, but with only a single base in agreement with the consensus. Note: Implies the depth of coverage = 1 ATTR_No_Conflict ATTR_Quality_Strand ATTR_Single_Coverage Consensus: A (A, 30, Forward) Quality Class 10 Low quality conflict, and at least one low quality base in both directions in agreement. ATTR_Non_Quality_Conflict ATTR_Non_Quality_Other_Strand Consensus: A (A, 20, Forward) (A, 20, Reverse) (T, 20, Reverse) Quality Class 11 No Conflict, but with only a single base in agreement. Note: Implies the depth of coverage = 1 ATTR_No_Conflict ATTR_Non_Quality_Strand ATTR_Single_Coverage Consensus: A (A, 20, Forward) Quality Class 12 Low quality conflict, and at least two low quality bases in the same direction in agreement. ATTR_Non_Quality_Conflict ATTR_Non_Quality_Same_Strand Consensus: A (A, 20, Forward) (A, 20, Forward) (T, 20, Reverse) Quality Class 13 Low quailty conflict, with only a single high quality base in agreement. ATTR_Non_Quality_Conflict ATTR_Quality_Strand ATTR_Single_Coverage Consensus: A (A, 35, Forward) (T, 10, Reverse) Quality Class 14 Low quality conflict, with only a single low quality base in agreement. ATTR_Non_Quality_Conflict ATTR_Non_Quality_Strand ATTR_Single_Coverage Consensus: A (A, 25, Forward) (T, 10, Reverse) Quality Class 15 High quality conflict, and at least one high quality base in both directions in agreement. ATTR_Quality_Conflict ATTR_Quality_Other_Strand Consensus: A (A, 30, Forward) (A, 30, Reverse) (T, 30, Reverse) Quality Class 16 High quality conflict, and at least one high quality base in one direction in agreement, and at least one low quality base in the other direction in agreement. ATTR_Quality_Conflict ATTR_Quality_Strand ATTR_Non_Quality_Other_Strand Consensus: A (A, 30, Forward) (A, 20, Reverse) (T, 30, Reverse) Quality Class 17 High quality conflict, and at least one high quality base in one direction in agreement, and some other base in the same direction in agreement. ATTR_Quality_Conflict ATTR_Quality_Strand ATTR_Any_Same_Strand Consensus: A (A, 30, Forward) (A, 20, Forward) (T, 30, Reverse) Quality Class 18 High quality conflict, and at least one low quality base in both directions in agreement. ATTR_Quality_Conflict ATTR_Non_Quality_Other_Strand Consensus: A (A, 25, Forward) (A, 25, Reverse) (T, 30, Reverse) Quality Class 19 High quality conflict, and at least two low quality bases in the same direction in agreement. ATTR_Quality_Conflict ATTR_Non_Quality_Same_Strand Consensus: A (A, 25, Forward) (A, 25, Forward) (T, 30, Reverse) Quality Class 20 High quality conflict, but with only a single high quality base in agreement. ATTR_Quality_Conflict ATTR_Quality_Strand ATTR_Single_Coverage Consensus: A (A, 40, Forward) (T, 30, Reverse) Quality Class 21 Consensus is ambiguous, and there is only a single base in agreement. ATTR_Ambiguity ATTR_Single_Coverage Consensus: M (M, 30, Forward) (A, 30, Forward) Quality Class 22 Consensus is ambiguous. ATTR_Ambiguity Consensus: M (A, 30, Forward) (C, 30, Forward) Quality Class 23 High quality conflict, and only one low quality read in agreement. Note: This is also the quality class used to indicate there are no reads that support that consensus. This can be an indication of a miscalled consensus. ATTR_Quality_Conflict ATTR_Non_Quality_Same_Strand ATTR_Single_Coverage OR: Not ATTR_Quality_Strand Not ATTR_Non_Quality_Strand Consensus: A Consensus: A (A, 20, Forward) (C, 30, Forward) (C, 30, Forward) (C, 30, Reverse) $Date: 2005/07/29 02:55:17 $