Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_TTAGGC_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:2463320
Total_Number_Of_Reads:	2463320
Number_of_Chastity_Passed_Reads:	2290468
Number_of_Chastity_Failed:	172852
Number_of_Duplicates:	2005924
Number_Reads_Aligned:	2024858
Number_Reads_Unaligned:	265610
Mapping_Qualities_of_Aligned:
	0:	58500
	1-9:	7184
	10-19:	53662
	20-29:	264899
	30-39:	26079
	40-49:	9518
	50-59:	456
	60-69:	1604560
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	1966358
Number_Non_Unique_Alignments:	58500
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1218846
	1_mismatches:	361976
	2_mismatches:	153529
	3_mismatches:	112831
Number_of_Paired_Alignments:	1999144
Average_Insert_Size:	234.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	1959174
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	17252
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	17206
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	5872
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	1959154
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1524
	10:	828
	11:	968
	12:	1121
	13:	200
	14:	530
	15:	494
	16:	525
	17:	944
	18:	256
	19:	1868
	2:	1488
	20:	512
	21:	121
	22:	379
	3:	647
	4:	624
	5:	727
	6:	646
	7:	1267
	8:	492
	9:	493
	X:	568
	Y:	30
Estimate_for_X_coverage:	0.000664
END