1.Base summary

QC result

Sample	sample
Read_length	150:150
Read_raw	853,942,950
Read_clean	851,531,716
Read_clean_Rate	99.72%
Q20_raw	95.36%
Q20_1_raw	96.01%
Q20_2_raw	94.71%
Q30_raw	86.35%
Q30_1_raw	87.62%
Q30_2_raw	85.09%
GC_raw	41.45%
Q20_clean	95.39%
Q20_1_clean	96.02%
Q20_2_clean	94.77%
Q30_clean	86.39%
Q30_1_clean	87.63%
Q30_2_clean	85.14%
GC_clean	41.44%
AT_1_Separation	0.20%
AT_2_Separation	0.10%
GC_1_Separation	0.20%
GC_2_Separation	0.10%

Base distribution

Base quality distribution

2.Alignment Information

Alignment result

Sample	sample
Mapping_Rate	99.31%
PE_Mapping_Rate	99.16%
Unique_Rate	94.81%
Duplication_Rate	1.81%
Mismatch_Rate	1.06%
Insert_size	371.9
Average_depth(rmdup)	42.57
Coverage(>=1X)	99.08%
Coverage(>=2X)	98.95%
Coverage(>=3X)	98.83%
Coverage(>=4X)	98.71%
Coverage(>=5X)	98.58%
Coverage(>=10X)	97.98%
Coverage(>=20X)	97.02%
Uniformity(>0.2f)	98.08%

Insert size distribution

Depth distribution

3.Variant calling

Variant statistics

Sample	sample
Total_SNP	3,866,081
dbSNP_rate	99.2%
Novel_SNP	30,876
Novel_SNP_Rate	0.8%
Ti/Tv	2
Total_INDEL	936,637
dbINDEL_Rate	97.31%

4.Variant evaluation

SNP evaluation

Threshold	True-pos-baseline	True-pos-call	False-pos	False-neg	Precision	Sensitivity	F-measure
1	3,201,433	3,201,440	16,177	8,817	0.9950	0.9973	0.9961
None	3,201,433	3,201,440	16,196	8,817	0.9950	0.9973	0.9961

INDEL evaluation

Threshold	True-pos-baseline	True-pos-call	False-pos	False-neg	Precision	Sensitivity	F-measure
15	476,806	476,807	3,328	4,456	0.9931	0.9907	0.9919
None	476,984	476,985	3,554	4,278	0.9926	0.9911	0.9919