BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094060.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 374,608 number of mapped reads = 355,592 (94.92%) number of supplementary alignments = 14,250 (3.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 178,678 number of mapped paired reads (second in pair) = 176,914 number of mapped paired reads (both in pair) = 352,950 number of mapped paired reads (singletons) = 2,642 number of mapped bases = 46,935,841 bp number of sequenced bases = 45,666,010 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 332,211 duplication rate = 50.58% >>>>>>> Insert size mean insert size = 739,925.5243 std insert size = 7,816,310.3954 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 43.8658 >>>>>>> ACTG content number of A's = 12,756,311 bp (27.93%) number of C's = 10,079,869 bp (22.07%) number of T's = 12,263,339 bp (26.85%) number of G's = 10,566,027 bp (23.14%) number of N's = 464 bp (0%) GC percentage = 45.21% >>>>>>> Mismatches and indels general error rate = 0.0463 number of mismatches = 2,057,582 number of insertions = 34,746 mapped reads with insertion percentage = 9.58% number of deletions = 162,303 mapped reads with deletion percentage = 42.69% homopolymer indels = 29.73% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 3.425X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 946787 0.003798534166941955 1.5403315304775265 chr2 243199373 1946551 0.008003930996976707 2.3418813216344523 chr3 198022430 1124922 0.00568078070751884 1.887281783722851 chr4 191154276 1043494 0.005458910058595812 1.5822744303709289 chr5 180915260 396966 0.0021942095984606273 0.6776093285852793 chr6 171115067 1042053 0.006089779341289683 2.6164161731617006 chr7 159138663 1402087 0.008810473668488718 2.4596479298350964 chr8 146364022 898957 0.006141926053384895 1.8426360019402461 chr9 141213431 668283 0.004732432285424748 1.8276085126800985 chr10 135534747 1371688 0.010120563400616374 3.2637760368911453 chr11 135006516 1431436 0.010602717871780352 2.9614095610759943 chr12 133851895 1772314 0.013240858487659065 3.6343690286468107 chr13 115169878 972103 0.008440601109258794 2.4730459716161963 chr14 107349540 216207 0.0020140468231163357 0.7878887539331916 chr15 102531392 527483 0.005144600006991029 1.3294633636015516 chr16 90354753 347765 0.003848884407884995 1.2171008036612068 chr17 81195210 1072339 0.01320692439861908 2.7188699346001295 chr18 78077248 161615 0.0020699371986061805 0.5205677732606662 chr19 59128983 299814 0.0050705083156935065 1.457028331844983 chr20 63025520 136846 0.002171279189763131 0.5019877625120007 chr21 48129895 81505 0.0016934381427592975 0.3644535428514259 chr22 51304566 71985 0.0014030914909211004 0.33503491957837345 chrMT 16571 2778766 167.68849194375716 675.2543413864227 chrX 155270560 25528908 0.16441563680842008 9.935352615135715 chrY 59373566 694967 0.011704990062412624 2.632360590393958