Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CCGTCC_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:1247118
Total_Number_Of_Reads:	1247118
Number_of_Chastity_Passed_Reads:	1162240
Number_of_Chastity_Failed:	84878
Number_of_Duplicates:	705232
Number_Reads_Aligned:	707829
Number_Reads_Unaligned:	454411
Mapping_Qualities_of_Aligned:
	0:	15091
	1-9:	3678
	10-19:	5215
	20-29:	27792
	30-39:	401067
	40-49:	17484
	50-59:	200
	60-69:	237302
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	692738
Number_Non_Unique_Alignments:	15091
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	570731
	1_mismatches:	58150
	2_mismatches:	21407
	3_mismatches:	14626
Number_of_Paired_Alignments:	293692
Average_Insert_Size:	212.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	689060
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	2454
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	2416
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	1394
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	688158
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	87
	10:	111
	11:	50
	12:	77
	13:	12
	14:	4
	15:	129
	16:	33
	17:	30
	18:	10
	19:	97
	2:	377
	20:	45
	21:	4
	22:	40
	3:	109
	4:	735
	5:	106
	6:	104
	7:	214
	8:	13
	9:	21
	X:	46
Estimate_for_X_coverage:	0.000091
END