Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_CTCAGA_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:4395302
Total_Number_Of_Reads:	4395302
Number_of_Chastity_Passed_Reads:	4070308
Number_of_Chastity_Failed:	324994
Number_of_Duplicates:	3909009
Number_Reads_Aligned:	3926179
Number_Reads_Unaligned:	144129
Mapping_Qualities_of_Aligned:
	0:	39825
	1-9:	2019
	10-19:	34331
	20-29:	297662
	30-39:	12796
	40-49:	3046
	50-59:	726
	60-69:	3535774
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	3886354
Number_Non_Unique_Alignments:	39825
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	2742689
	1_mismatches:	610529
	2_mismatches:	176750
	3_mismatches:	188821
Number_of_Paired_Alignments:	3913720
Average_Insert_Size:	221.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	3884335
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	14889
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	14841
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	5150
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	3884332
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1616
	10:	527
	11:	637
	12:	920
	13:	144
	14:	662
	15:	328
	16:	672
	17:	1019
	18:	148
	19:	1454
	2:	741
	20:	326
	21:	107
	22:	475
	3:	570
	4:	505
	5:	331
	6:	685
	7:	1600
	8:	440
	9:	479
	X:	473
	Y:	30
Estimate_for_X_coverage:	0.000602
END