Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_GCACTT_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:5258054
Total_Number_Of_Reads:	5258054
Number_of_Chastity_Passed_Reads:	4617998
Number_of_Chastity_Failed:	640056
Number_of_Duplicates:	4245065
Number_Reads_Aligned:	4264609
Number_Reads_Unaligned:	353389
Mapping_Qualities_of_Aligned:
	0:	6927
	1-9:	48
	10-19:	20008
	20-29:	1227357
	30-39:	3251
	40-49:	38
	50-59:	1552
	60-69:	3005428
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	4257682
Number_Non_Unique_Alignments:	6927
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	2491790
	1_mismatches:	887726
	2_mismatches:	304935
	3_mismatches:	137588
Number_of_Paired_Alignments:	4258078
Average_Insert_Size:	223.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	4257634
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	18934
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	18912
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	6320
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	4257625
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1839
	10:	522
	11:	966
	12:	828
	13:	339
	14:	312
	15:	447
	16:	531
	17:	1267
	18:	570
	19:	1959
	2:	924
	20:	219
	21:	770
	22:	358
	3:	832
	4:	565
	5:	640
	6:	1705
	7:	1824
	8:	443
	9:	433
	X:	621
	Y:	20
Estimate_for_X_coverage:	0.000686
END