Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CACGAT_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:6099218
Total_Number_Of_Reads:	6099218
Number_of_Chastity_Passed_Reads:	5656758
Number_of_Chastity_Failed:	442460
Number_of_Duplicates:	5439455
Number_Reads_Aligned:	5460278
Number_Reads_Unaligned:	196480
Mapping_Qualities_of_Aligned:
	0:	51920
	1-9:	3698
	10-19:	45944
	20-29:	308562
	30-39:	18020
	40-49:	4900
	50-59:	1032
	60-69:	5026202
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	5408358
Number_Non_Unique_Alignments:	51920
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	4070701
	1_mismatches:	731336
	2_mismatches:	239260
	3_mismatches:	188895
Number_of_Paired_Alignments:	5443162
Average_Insert_Size:	223.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	5404660
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	18495
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	18428
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	6800
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	5404642
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	2081
	10:	785
	11:	783
	12:	1128
	13:	198
	14:	782
	15:	407
	16:	876
	17:	1031
	18:	192
	19:	1754
	2:	866
	20:	388
	21:	158
	22:	579
	3:	806
	4:	605
	5:	459
	6:	729
	7:	2039
	8:	657
	9:	585
	X:	569
	Y:	38
Estimate_for_X_coverage:	0.000731
END