Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_ACGATA_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:3250538
Total_Number_Of_Reads:	3250538
Number_of_Chastity_Passed_Reads:	2973054
Number_of_Chastity_Failed:	277484
Number_of_Duplicates:	2898486
Number_Reads_Aligned:	2915511
Number_Reads_Unaligned:	57543
Mapping_Qualities_of_Aligned:
	0:	6888
	1-9:	130
	10-19:	15860
	20-29:	567690
	30-39:	2431
	40-49:	844
	50-59:	1248
	60-69:	2320420
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	2908623
Number_Non_Unique_Alignments:	6888
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1790163
	1_mismatches:	621177
	2_mismatches:	138475
	3_mismatches:	62615
Number_of_Paired_Alignments:	2913356
Average_Insert_Size:	224.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	2908493
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	15089
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	15070
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	4550
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	2908493
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1397
	10:	664
	11:	753
	12:	1232
	13:	181
	14:	412
	15:	289
	16:	817
	17:	972
	18:	182
	19:	1258
	2:	922
	20:	300
	21:	327
	22:	429
	3:	757
	4:	423
	5:	342
	6:	599
	7:	1483
	8:	388
	9:	456
	X:	498
	Y:	8
Estimate_for_X_coverage:	0.000597
END