Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_AAGACT_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:6539080
Total_Number_Of_Reads:	6539080
Number_of_Chastity_Passed_Reads:	6046176
Number_of_Chastity_Failed:	492904
Number_of_Duplicates:	5904295
Number_Reads_Aligned:	5922560
Number_Reads_Unaligned:	123616
Mapping_Qualities_of_Aligned:
	0:	2928
	1-9:	63
	10-19:	26803
	20-29:	532467
	30-39:	2321
	40-49:	18
	50-59:	714
	60-69:	5357246
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	5919632
Number_Non_Unique_Alignments:	2928
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	3963186
	1_mismatches:	761822
	2_mismatches:	235631
	3_mismatches:	665474
Number_of_Paired_Alignments:	5915244
Average_Insert_Size:	225.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	5919569
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	17730
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	17714
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	5174
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	5919569
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1632
	10:	1217
	11:	486
	12:	1248
	13:	391
	14:	414
	15:	585
	16:	596
	17:	830
	18:	323
	19:	1218
	2:	1003
	20:	397
	21:	139
	22:	179
	3:	985
	4:	896
	5:	490
	6:	1408
	7:	1280
	8:	568
	9:	525
	X:	904
	Y:	16
Estimate_for_X_coverage:	0.000641
END