Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_ACTCTC_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:2628440
Total_Number_Of_Reads:	2628440
Number_of_Chastity_Passed_Reads:	2466854
Number_of_Chastity_Failed:	161586
Number_of_Duplicates:	2229983
Number_Reads_Aligned:	2236980
Number_Reads_Unaligned:	229874
Mapping_Qualities_of_Aligned:
	0:	297
	1-9:	12
	10-19:	40
	20-29:	2281
	30-39:	201874
	40-49:	1426
	50-59:	66
	60-69:	2030984
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2236683
Number_Non_Unique_Alignments:	297
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1615794
	1_mismatches:	434583
	2_mismatches:	47417
	3_mismatches:	117672
Number_of_Paired_Alignments:	2034354
Average_Insert_Size:	229.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2236671
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	6835
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	6829
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	4650
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2236639
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	472
	10:	426
	11:	306
	12:	660
	13:	107
	14:	146
	15:	202
	16:	312
	17:	430
	18:	69
	19:	406
	2:	475
	20:	171
	21:	63
	22:	232
	3:	509
	4:	153
	5:	201
	6:	534
	7:	408
	8:	174
	9:	168
	X:	209
	Y:	2
Estimate_for_X_coverage:	0.000246
END