BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472488.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 34,314,096 number of mapped reads = 33,900,725 (98.8%) number of supplementary alignments = 137,995 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,998,754 number of mapped paired reads (second in pair) = 16,901,971 number of mapped paired reads (both in pair) = 33,694,570 number of mapped paired reads (singletons) = 206,155 number of mapped bases = 3,336,038,507 bp number of sequenced bases = 3,335,607,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,903,092 duplication rate = 47.71% >>>>>>> Insert size mean insert size = 32,211.3777 std insert size = 1,754,231.0052 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 55.0618 >>>>>>> ACTG content number of A's = 922,353,983 bp (27.65%) number of C's = 749,276,464 bp (22.46%) number of T's = 917,845,551 bp (27.52%) number of G's = 745,611,962 bp (22.35%) number of N's = 519,589 bp (0.02%) GC percentage = 44.82% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 19,751,551 number of insertions = 183,455 mapped reads with insertion percentage = 0.54% number of deletions = 174,668 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.96% >>>>>>> Coverage mean coverageData = 1.0776X std coverageData = 30.1714X There is a 10.5% of reference with a coverageData >= 1X There is a 4.83% of reference with a coverageData >= 2X There is a 2.04% of reference with a coverageData >= 3X There is a 1.29% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.67% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.36% of reference with a coverageData >= 21X There is a 0.35% of reference with a coverageData >= 22X There is a 0.35% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.34% of reference with a coverageData >= 25X There is a 0.33% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.3% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.27% of reference with a coverageData >= 46X There is a 0.26% of reference with a coverageData >= 47X There is a 0.26% of reference with a coverageData >= 48X There is a 0.26% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 363726675 1.4592809178998996 42.560883678818634 chr2 243199373 209882731 0.8630068754330218 23.44663659365283 chr3 198022430 369178701 1.864327697624961 33.924752610776736 chr4 191154276 129101919 0.6753807537112065 20.471731041610045 chr5 180915260 163359883 0.9029635366303539 25.225428031166786 chr6 171115067 213434735 1.247317017384565 28.37682872948354 chr7 159138663 136694993 0.8589678361191209 22.869802958588537 chr8 146364022 151239115 1.0333080010605338 28.422913176669276 chr9 141213431 217133119 1.537623705212573 36.3308281089547 chr10 135534747 78927465 0.5823411836966058 17.142227598451964 chr11 135006516 148381573 1.0990697145314083 31.923342856005625 chr12 133851895 165014468 1.232813835022657 31.402256481319224 chr13 115169878 101380923 0.880272904343964 32.75856862110459 chr14 107349540 87068876 0.8110782402980022 22.687651560920962 chr15 102531392 119668601 1.1671410937247395 35.61601464435831 chr16 90354753 94479561 1.0456512564424807 21.991170011586743 chr17 81195210 117865347 1.4516293140937748 33.112231092326546 chr18 78077248 56304986 0.7211446028425592 20.36920553366198 chr19 59128983 70199574 1.1872278270032144 30.222715797159942 chr20 63025520 68076832 1.080147089623378 28.01003743010264 chr21 48129895 13781608 0.28634195025773485 10.930098168034734 chr22 51304566 32347408 0.6304976442057808 14.984036692607566 chrMT 16571 4448 0.2684207350190091 0.7593905338493315 chrX 155270560 224165069 1.4437061925969739 49.411895461009834 chrY 59373566 4619897 0.07781067082950685 2.499753561713173