Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_TATAAT_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:2080078
Total_Number_Of_Reads:	2080078
Number_of_Chastity_Passed_Reads:	1842086
Number_of_Chastity_Failed:	237992
Number_of_Duplicates:	1780960
Number_Reads_Aligned:	1790123
Number_Reads_Unaligned:	51963
Mapping_Qualities_of_Aligned:
	0:	3788
	1-9:	59
	10-19:	8998
	20-29:	387557
	30-39:	935
	40-49:	24
	50-59:	280
	60-69:	1388482
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	1786335
Number_Non_Unique_Alignments:	3788
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1278204
	1_mismatches:	259075
	2_mismatches:	52626
	3_mismatches:	25904
Number_of_Paired_Alignments:	1788322
Average_Insert_Size:	225.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	1786276
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	8681
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	8665
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	3098
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	1786226
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	456
	10:	200
	11:	393
	12:	400
	13:	318
	14:	168
	15:	293
	16:	452
	17:	497
	18:	128
	19:	802
	2:	424
	20:	473
	21:	62
	22:	172
	3:	465
	4:	684
	5:	452
	6:	398
	7:	706
	8:	257
	9:	266
	X:	211
	Y:	4
Estimate_for_X_coverage:	0.000322
END