Script_path:	/home/rcorbett/slx_service_rc/tags/0.0.8/bamStats.py
Bam_path:	/projects/remc_bigdata/Karsan/HS1235_ctl/maq2sam/HS1235.h.sorted.bam
Quality_threshold:	10
Read_length:	75
Total_Number_Of_Reads:	21753664
Number_of_Chastity_Passed_Reads:	21753664
Number_of_Chastity_Failed:	0
Number_of_Duplicates:	0
Number_Reads_Aligned:	21753664
Number_Reads_Unaligned:	0
Mapping_Qualities_of_Aligned:
	0:	1808487
	1-9:	244915
	10-19:	769225
	20-29:	1565887
	30-39:	2759651
	40-49:	1746412
	50-59:	1905356
	60-69:	4040524
	70-79:	6206080
	80-89:	707127
Number_Unique_Alignments:	19945177
Number_Non_Unique_Alignments:	1808487
Number_Mismatches_in_Unique_Alignments:
	0_mismatches:	8341288
	1_mismatches:	4958438
	2_mismatches:	1843456
	3_mismatches:	1288122
Number_of_Paired_Alignments:	0
Average_Insert_Size:	0.000000
Number_of_Uniquely_Aligned_Reads_with_Q_>=_10:	19700262
Number_of_Uniquely_Aligned_Reads_without_Dups_Q_>_0:	19945177
Number_of_Uniquely_Aligned_Reads_without_Dups_and_Q_>=_10:	19700262
Number_of_Reads_Used_for_SNV_calling_with_Q_>=_10:	19700262
Number_of_Reads_Used_for_Gene_Coverage_with_Q_>=_10:	19678475
Number_Uniquely_Aligned_Without_Dups_to_Each_Chr:
	1:	1820293
	10:	1017874
	11:	1082845
	12:	857270
	13:	569303
	14:	649073
	15:	528764
	16:	366998
	17:	693946
	18:	433546
	19:	444901
	2:	1691452
	20:	529898
	21:	211308
	22:	192345
	3:	1350757
	4:	1222106
	5:	1325537
	6:	1546358
	7:	1145419
	8:	909807
	9:	728994
	MT:	669
	X:	617886
	Y:	7828
Estimate_for_X_coverage:	0.572465
END