BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006084.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,288,266 number of mapped reads = 7,919,152 (85.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,009,928 number of mapped paired reads (second in pair) = 3,909,224 number of mapped paired reads (both in pair) = 7,131,254 number of mapped paired reads (singletons) = 787,898 number of mapped bases = 304,681,582 bp number of sequenced bases = 304,647,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,201,363 duplication rate = 13.68% >>>>>>> Insert size mean insert size = 89,811.4478 std insert size = 2,975,573.689 median insert size = 94 >>>>>>> Mapping quality mean mapping quality = 45.5597 >>>>>>> ACTG content number of A's = 79,779,297 bp (26.19%) number of C's = 68,180,113 bp (22.38%) number of T's = 83,486,258 bp (27.4%) number of G's = 73,189,829 bp (24.02%) number of N's = 12,327 bp (0%) GC percentage = 46.4% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,629,806 number of insertions = 11,400 mapped reads with insertion percentage = 0.14% number of deletions = 26,759 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.0984X std coverageData = 0.7648X There is a 3.32% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 1.38% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% 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% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 26204013 0.10513118440736001 0.8823391111170086 chr2 243199373 26184709 0.107667666560966 0.7946937920468705 chr3 198022430 20608426 0.10407117011946576 0.7256692715427876 chr4 191154276 17988940 0.09410691916721758 0.7100774211769678 chr5 180915260 18126795 0.10019494762354486 0.7129511501510388 chr6 171115067 17350457 0.10139643050836664 0.7800532705251405 chr7 159138663 16749645 0.10525188966806891 0.8515715748884763 chr8 146364022 14829227 0.10131743305058943 0.7857983836462228 chr9 141213431 13201424 0.09348561186081514 0.7035837904652806 chr10 135534747 14732617 0.10869992622629826 0.7665675320732728 chr11 135006516 14034972 0.10395773786207474 1.0172761910082235 chr12 133851895 14094958 0.10530264065368668 0.7385799148353623 chr13 115169878 9036626 0.07846345031293686 0.6350017290531925 chr14 107349540 9481733 0.08832579068340675 0.6759984314483227 chr15 102531392 9445394 0.09212197177621465 0.6919882870140674 chr16 90354753 10119129 0.11199332258702539 0.7713383117042828 chr17 81195210 9863371 0.12147725216795424 0.8297253272040692 chr18 78077248 7691678 0.0985136924908009 0.7720090162008912 chr19 59128983 7823149 0.1323065035635739 0.9568297558430171 chr20 63025520 7478117 0.11865220628088431 0.7989049552657056 chr21 48129895 4045229 0.0840481575951911 0.6922426067735865 chr22 51304566 4627922 0.09020487572197765 0.7057915338536647 chrMT 16571 20232 1.220928127451572 2.827664353765105 chrX 155270560 9015036 0.05806017573453719 0.5364103716234473 chrY 59373566 1927783 0.0324687083811001 0.3847907789272818