Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_AAGCGA_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:4289832
Total_Number_Of_Reads:	4289832
Number_of_Chastity_Passed_Reads:	3931166
Number_of_Chastity_Failed:	358666
Number_of_Duplicates:	2744369
Number_Reads_Aligned:	2754454
Number_Reads_Unaligned:	1176712
Mapping_Qualities_of_Aligned:
	0:	70677
	1-9:	7171
	10-19:	14779
	20-29:	241861
	30-39:	947762
	40-49:	16162
	50-59:	184
	60-69:	1455858
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2683777
Number_Non_Unique_Alignments:	70677
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1469461
	1_mismatches:	560594
	2_mismatches:	118980
	3_mismatches:	48283
Number_of_Paired_Alignments:	2031792
Average_Insert_Size:	218.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2676606
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	9511
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	9438
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	4060
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2675714
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1071
	10:	382
	11:	438
	12:	490
	13:	133
	14:	133
	15:	295
	16:	632
	17:	418
	18:	114
	19:	507
	2:	1138
	20:	142
	21:	177
	22:	196
	3:	382
	4:	199
	5:	260
	6:	776
	7:	777
	8:	185
	9:	243
	X:	419
	Y:	4
Estimate_for_X_coverage:	0.000354
END