Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CTTGTA_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:3621886
Total_Number_Of_Reads:	3621886
Number_of_Chastity_Passed_Reads:	3329186
Number_of_Chastity_Failed:	292700
Number_of_Duplicates:	3268539
Number_Reads_Aligned:	3279674
Number_Reads_Unaligned:	49512
Mapping_Qualities_of_Aligned:
	0:	6674
	1-9:	131
	10-19:	15320
	20-29:	540049
	30-39:	2236
	40-49:	902
	50-59:	1428
	60-69:	2712934
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	3273000
Number_Non_Unique_Alignments:	6674
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	2107400
	1_mismatches:	670755
	2_mismatches:	154695
	3_mismatches:	66427
Number_of_Paired_Alignments:	3278080
Average_Insert_Size:	225.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	3272869
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	10072
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	10056
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	3272
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	3272869
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	868
	10:	558
	11:	524
	12:	732
	13:	93
	14:	239
	15:	196
	16:	648
	17:	539
	18:	71
	19:	857
	2:	383
	20:	207
	21:	269
	22:	290
	3:	629
	4:	281
	5:	271
	6:	432
	7:	877
	8:	299
	9:	330
	X:	477
	Y:	2
Estimate_for_X_coverage:	0.000391
END