Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_GGCTAC_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:2984444
Total_Number_Of_Reads:	2984444
Number_of_Chastity_Passed_Reads:	2806334
Number_of_Chastity_Failed:	178110
Number_of_Duplicates:	2732034
Number_Reads_Aligned:	2742319
Number_Reads_Unaligned:	64015
Mapping_Qualities_of_Aligned:
	0:	54739
	1-9:	8665
	10-19:	30715
	20-29:	1491440
	30-39:	212004
	40-49:	3628
	50-59:	104
	60-69:	941024
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2687580
Number_Non_Unique_Alignments:	54739
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1380180
	1_mismatches:	376303
	2_mismatches:	139768
	3_mismatches:	73717
Number_of_Paired_Alignments:	2522846
Average_Insert_Size:	221.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2678915
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	9654
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	9553
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	2328
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2678898
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	661
	10:	696
	11:	224
	12:	466
	13:	87
	14:	188
	15:	253
	16:	295
	17:	399
	18:	112
	19:	526
	2:	1453
	20:	165
	21:	54
	22:	212
	3:	484
	4:	855
	5:	265
	6:	500
	7:	1198
	8:	150
	9:	207
	X:	204
Estimate_for_X_coverage:	0.000361
END