Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_TGACCA_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:4615566
Total_Number_Of_Reads:	4615566
Number_of_Chastity_Passed_Reads:	4224638
Number_of_Chastity_Failed:	390928
Number_of_Duplicates:	4169056
Number_Reads_Aligned:	4177299
Number_Reads_Unaligned:	47339
Mapping_Qualities_of_Aligned:
	0:	718
	1-9:	47
	10-19:	8632
	20-29:	298094
	30-39:	1360
	40-49:	14
	50-59:	818
	60-69:	3867616
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	4176581
Number_Non_Unique_Alignments:	718
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	2895304
	1_mismatches:	578263
	2_mismatches:	151979
	3_mismatches:	362795
Number_of_Paired_Alignments:	4175398
Average_Insert_Size:	226.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	4176534
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	8026
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	8014
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	3288
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	4176534
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	450
	10:	637
	11:	162
	12:	717
	13:	93
	14:	302
	15:	296
	16:	325
	17:	211
	18:	56
	19:	643
	2:	280
	20:	82
	21:	45
	22:	101
	3:	483
	4:	324
	5:	233
	6:	791
	7:	650
	8:	210
	9:	317
	X:	618
Estimate_for_X_coverage:	0.000289
END