Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CACCGG_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:3606194
Total_Number_Of_Reads:	3606194
Number_of_Chastity_Passed_Reads:	3319928
Number_of_Chastity_Failed:	286266
Number_of_Duplicates:	3036764
Number_Reads_Aligned:	3043770
Number_Reads_Unaligned:	276158
Mapping_Qualities_of_Aligned:
	0:	288
	1-9:	14
	10-19:	38
	20-29:	2936
	30-39:	223082
	40-49:	1762
	50-59:	56
	60-69:	2815594
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	3043482
Number_Non_Unique_Alignments:	288
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	2250201
	1_mismatches:	540153
	2_mismatches:	62463
	3_mismatches:	161329
Number_of_Paired_Alignments:	2819732
Average_Insert_Size:	229.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	3043468
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	6836
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	6830
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	4680
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	3043439
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	475
	10:	427
	11:	345
	12:	706
	13:	94
	14:	138
	15:	174
	16:	276
	17:	493
	18:	69
	19:	418
	2:	479
	20:	138
	21:	49
	22:	231
	3:	506
	4:	110
	5:	146
	6:	587
	7:	435
	8:	168
	9:	149
	X:	220
	Y:	3
Estimate_for_X_coverage:	0.000246
END