BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926922.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 15,472,624 number of mapped reads = 15,126,256 (97.76%) number of supplementary alignments = 193,674 (1.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,580,519 number of mapped paired reads (second in pair) = 7,545,737 number of mapped paired reads (both in pair) = 14,963,412 number of mapped paired reads (singletons) = 162,844 number of mapped bases = 1,416,525,355 bp number of sequenced bases = 1,415,414,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 816,875 duplication rate = 4.17% >>>>>>> Insert size mean insert size = 125,076.5901 std insert size = 3,443,028.141 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.3275 >>>>>>> ACTG content number of A's = 402,941,379 bp (28.47%) number of C's = 282,995,702 bp (19.99%) number of T's = 408,523,919 bp (28.86%) number of G's = 320,658,573 bp (22.65%) number of N's = 295,175 bp (0.02%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 13,463,083 number of insertions = 234,335 mapped reads with insertion percentage = 1.52% number of deletions = 774,054 mapped reads with deletion percentage = 4.98% homopolymer indels = 52.69% >>>>>>> Coverage mean coverageData = 0.4576X std coverageData = 1.9998X There is a 24% of reference with a coverageData >= 1X There is a 10.67% of reference with a coverageData >= 2X There is a 4.91% of reference with a coverageData >= 3X There is a 2.46% of reference with a coverageData >= 4X There is a 1.28% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 113643994 0.4559426714527624 2.2015002762224674 chr2 243199373 123488045 0.5077646520083751 3.1229298095442255 chr3 198022430 95375131 0.4816380194910243 1.0958360217644543 chr4 191154276 84875916 0.4440178779992345 1.7669739860515348 chr5 180915260 87123330 0.4815698244581469 1.0775988262751177 chr6 171115067 83412634 0.487465162842732 2.355242351611282 chr7 159138663 72401845 0.4549607470310342 1.4875853601734068 chr8 146364022 70820057 0.4838624686058436 1.245915991722614 chr9 141213431 59632872 0.4222889535202923 2.1794791705619976 chr10 135534747 70374791 0.5192380002745717 4.4180797078446545 chr11 135006516 68181274 0.5050220983407941 1.5694722078805585 chr12 133851895 61823807 0.4618821944956401 1.0797411309867133 chr13 115169878 42915244 0.37262559225772557 0.9451300033943173 chr14 107349540 42070322 0.39190034722086375 1.0025601956395842 chr15 102531392 43265351 0.4219717508565572 1.0539809319971893 chr16 90354753 46406795 0.5136065725286195 2.9897730723490916 chr17 81195210 37046038 0.45625890985441137 1.351791904180494 chr18 78077248 38271925 0.49018025071785315 2.138249050242807 chr19 59128983 23434623 0.3963305609365884 1.5835957662274545 chr20 63025520 34229748 0.5431093309503833 1.27417309019031 chr21 48129895 18532216 0.3850458431293066 1.3896869607184947 chr22 51304566 16374983 0.31917204016500206 0.9499063366022285 chrMT 16571 518688 31.300947438295818 24.710279590213304 chrX 155270560 79987252 0.5151475720832075 1.2410652001077533 chrY 59373566 2318474 0.0390489262511199 1.3759003734067692