1.Base summary

QC result

Sample	Sample
Base_raw	11,291,464,704
Read_length	150:150
Read_raw	75,276,432
Read_clean	74,509,504
Read_clean_Rate	98.98%
Q20_raw	95.14%
Q20_1_raw	95.87%
Q20_2_raw	94.42%
Q30_raw	86.31%
Q30_1_raw	87.84%
Q30_2_raw	84.79%
GC_raw	43.48%
Q20_clean	95.18%
Q20_1_clean	95.93%
Q20_2_clean	94.42%
Q30_clean	86.34%
Q30_1_clean	87.89%
Q30_2_clean	84.8%
GC_clean	43.54%

Base distribution

Base quality distribution

2.Alignment Information

Alignment result

Sample	Sample
Mapping_Rate	99.29%
PE_Mapping_Rate	98.74%
Unique_Rate	93.02%
Duplication_Rate	5.63%
Mismatch_Rate	0.92%
Chimerical_Rate	1.67%
Insert_size	302.7
Capture_Rate_on_Reads	75.41%
Capture_Rate_on_Bases	66.31%
Average_depth(rmdup)	100.76
Coverage(>=1X)	99.01%
Coverage(>=4X)	98.17%
Coverage(>=10X)	96.68%
Coverage(>=20X)	92.39%
Coverage(>=30X)	85.12%
Coverage(>=100X)	34.29%
Uniformity(>0.2f)	91.78%
FOLD_80_BASE_PENALTY	2.879

Insert size distribution

Depth distribution

3.Variant calling

Variant statistics

Sample	Sample
Total_SNP	65,806
dbSNP_Rate	98.92%
Novel_SNP	712
Novel_SNP_Rate	1.08%
Ti/Tv	2.48
Total_InDel	7,313
dbInDel_Rate	68.58%

4.Variant evaluation

SNP evaluation

Threshold	True-pos-baseline	True-pos-call	False-pos	False-neg	Precision	Sensitivity	F-measure
6	54,670	54,670	75	1,127	0.9986	0.9798	0.9891
None	54,671	54,671	78	1,126	0.9986	0.9798	0.9891

InDel evaluation

Threshold	True-pos-baseline	True-pos-call	False-pos	False-neg	Precision	Sensitivity	F-measure
8	4,486	4,486	384	741	0.9211	0.8582	0.8886
None	4,497	4,497	407	730	0.9170	0.8603	0.8878