Script_path:	/home/rcorbett/slx_service_rc/trunk/bamStats.py
Bam_path:	/projects/NBL/amplicon_val/s_8_TGCTGG_paired.dup.sorted.bam
Quality_threshold:	40
Read_length:	100:1625760
Total_Number_Of_Reads:	1625760
Number_of_Chastity_Passed_Reads:	1491534
Number_of_Chastity_Failed:	134226
Number_of_Duplicates:	1439957
Number_Reads_Aligned:	1446389
Number_Reads_Unaligned:	45145
Mapping_Qualities_of_Aligned:
	0:	6614
	1-9:	1551
	10-19:	19094
	20-29:	156224
	30-39:	2104
	40-49:	1560
	50-59:	386
	60-69:	1258856
	70-79:	0
	80-89:	0
Number_Unique_Alignments:	1439775
Number_Non_Unique_Alignments:	6614
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	1054379
	1_mismatches:	184536
	2_mismatches:	94851
	3_mismatches:	42360
Number_of_Paired_Alignments:	1443260
Average_Insert_Size:	234.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	1438224
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	6100
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	6087
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_40:	2184
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	1438219
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	464
	10:	213
	11:	407
	12:	459
	13:	56
	14:	243
	15:	228
	16:	126
	17:	438
	18:	49
	19:	802
	2:	331
	20:	171
	21:	24
	22:	167
	3:	254
	4:	176
	5:	242
	6:	229
	7:	525
	8:	103
	9:	191
	X:	199
	Y:	3
Estimate_for_X_coverage:	0.000226
END