Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CCCATG_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:3094552
Total_Number_Of_Reads:	3094552
Number_of_Chastity_Passed_Reads:	2800018
Number_of_Chastity_Failed:	294534
Number_of_Duplicates:	2734310
Number_Reads_Aligned:	2742404
Number_Reads_Unaligned:	57614
Mapping_Qualities_of_Aligned:
	0:	435
	1-9:	43
	10-19:	13531
	20-29:	138386
	30-39:	1475
	40-49:	40
	50-59:	1790
	60-69:	2586704
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2741969
Number_Non_Unique_Alignments:	435
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1476056
	1_mismatches:	860510
	2_mismatches:	197412
	3_mismatches:	84297
Number_of_Paired_Alignments:	2740866
Average_Insert_Size:	225.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2741926
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	7834
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	7829
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	3384
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2741879
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	729
	10:	382
	11:	394
	12:	586
	13:	313
	14:	157
	15:	183
	16:	418
	17:	314
	18:	82
	19:	697
	2:	321
	20:	120
	21:	35
	22:	105
	3:	395
	4:	461
	5:	352
	6:	405
	7:	723
	8:	294
	9:	224
	X:	126
	Y:	18
Estimate_for_X_coverage:	0.000284
END