Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_ATACGG_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:4160284
Total_Number_Of_Reads:	4160284
Number_of_Chastity_Passed_Reads:	3758762
Number_of_Chastity_Failed:	401522
Number_of_Duplicates:	3655330
Number_Reads_Aligned:	3668099
Number_Reads_Unaligned:	90663
Mapping_Qualities_of_Aligned:
	0:	677
	1-9:	70
	10-19:	18368
	20-29:	199027
	30-39:	2089
	40-49:	74
	50-59:	2456
	60-69:	3445338
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	3667422
Number_Non_Unique_Alignments:	677
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	2019917
	1_mismatches:	1113669
	2_mismatches:	256600
	3_mismatches:	109886
Number_of_Paired_Alignments:	3665768
Average_Insert_Size:	225.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	3667352
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	12336
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	12310
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	5106
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	3667332
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1362
	10:	510
	11:	552
	12:	899
	13:	469
	14:	268
	15:	308
	16:	617
	17:	405
	18:	152
	19:	970
	2:	569
	20:	232
	21:	80
	22:	217
	3:	693
	4:	703
	5:	484
	6:	722
	7:	1045
	8:	454
	9:	379
	X:	223
	Y:	23
Estimate_for_X_coverage:	0.000448
END