Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CTGCTG_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:2786770
Total_Number_Of_Reads:	2786770
Number_of_Chastity_Passed_Reads:	2474332
Number_of_Chastity_Failed:	312438
Number_of_Duplicates:	2390872
Number_Reads_Aligned:	2403673
Number_Reads_Unaligned:	70659
Mapping_Qualities_of_Aligned:
	0:	4180
	1-9:	85
	10-19:	13389
	20-29:	489913
	30-39:	1234
	40-49:	16
	50-59:	492
	60-69:	1894364
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2399493
Number_Non_Unique_Alignments:	4180
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1709216
	1_mismatches:	358115
	2_mismatches:	77924
	3_mismatches:	37710
Number_of_Paired_Alignments:	2401558
Average_Insert_Size:	225.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2399408
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	12221
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	12205
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	4036
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2399325
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	757
	10:	488
	11:	496
	12:	608
	13:	444
	14:	256
	15:	339
	16:	742
	17:	558
	18:	204
	19:	1104
	2:	555
	20:	564
	21:	88
	22:	232
	3:	787
	4:	806
	5:	548
	6:	504
	7:	986
	8:	411
	9:	422
	X:	315
	Y:	7
Estimate_for_X_coverage:	0.000449
END