Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_ATAATT_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:3493002
Total_Number_Of_Reads:	3493002
Number_of_Chastity_Passed_Reads:	3211314
Number_of_Chastity_Failed:	281688
Number_of_Duplicates:	2688105
Number_Reads_Aligned:	2703825
Number_Reads_Unaligned:	507489
Mapping_Qualities_of_Aligned:
	0:	173556
	1-9:	5053
	10-19:	78331
	20-29:	1318180
	30-39:	307851
	40-49:	7548
	50-59:	70
	60-69:	813236
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2530269
Number_Non_Unique_Alignments:	173556
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	985797
	1_mismatches:	747366
	2_mismatches:	263504
	3_mismatches:	82955
Number_of_Paired_Alignments:	2250724
Average_Insert_Size:	205.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2525216
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	14735
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	14670
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	2412
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2525172
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1081
	10:	586
	11:	638
	12:	923
	13:	287
	14:	303
	15:	444
	16:	798
	17:	830
	18:	198
	19:	744
	2:	1477
	20:	376
	21:	220
	22:	238
	3:	746
	4:	570
	5:	493
	6:	1133
	7:	1250
	8:	442
	9:	519
	X:	425
	Y:	14
Estimate_for_X_coverage:	0.000552
END