Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_GAGTGG_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:3148360
Total_Number_Of_Reads:	3148360
Number_of_Chastity_Passed_Reads:	2841586
Number_of_Chastity_Failed:	306774
Number_of_Duplicates:	2385012
Number_Reads_Aligned:	2405448
Number_Reads_Unaligned:	436138
Mapping_Qualities_of_Aligned:
	0:	15362
	1-9:	86
	10-19:	27951
	20-29:	748216
	30-39:	1535
	40-49:	20
	50-59:	632
	60-69:	1611646
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2390086
Number_Non_Unique_Alignments:	15362
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1433179
	1_mismatches:	414038
	2_mismatches:	224383
	3_mismatches:	87043
Number_of_Paired_Alignments:	2398364
Average_Insert_Size:	221.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2390000
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	19408
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	19396
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	3932
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2389801
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	2129
	10:	703
	11:	928
	12:	1005
	13:	548
	14:	379
	15:	546
	16:	657
	17:	1035
	18:	429
	19:	1470
	2:	1027
	20:	328
	21:	517
	22:	411
	3:	968
	4:	815
	5:	719
	6:	1548
	7:	1520
	8:	618
	9:	571
	X:	517
	Y:	20
Estimate_for_X_coverage:	0.000717
END