BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926893.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 = 42,479,856 number of mapped reads = 39,613,568 (93.25%) number of supplementary alignments = 655,328 (1.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,833,854 number of mapped paired reads (second in pair) = 19,779,714 number of mapped paired reads (both in pair) = 39,153,802 number of mapped paired reads (singletons) = 459,766 number of mapped bases = 3,728,781,093 bp number of sequenced bases = 3,725,894,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,898,918 duplication rate = 7.96% >>>>>>> Insert size mean insert size = 122,310.4976 std insert size = 3,436,494.1572 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 53.1514 >>>>>>> ACTG content number of A's = 1,068,963,457 bp (28.69%) number of C's = 753,784,337 bp (20.23%) number of T's = 1,071,742,045 bp (28.76%) number of G's = 831,152,854 bp (22.31%) number of N's = 251,348 bp (0.01%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 35,417,835 number of insertions = 599,086 mapped reads with insertion percentage = 1.49% number of deletions = 2,047,765 mapped reads with deletion percentage = 5.03% homopolymer indels = 52.89% >>>>>>> Coverage mean coverageData = 1.2045X std coverageData = 5.3838X There is a 36.79% of reference with a coverageData >= 1X There is a 24.02% of reference with a coverageData >= 2X There is a 15.64% of reference with a coverageData >= 3X There is a 10.88% of reference with a coverageData >= 4X There is a 7.73% of reference with a coverageData >= 5X There is a 5.62% of reference with a coverageData >= 6X There is a 4.15% of reference with a coverageData >= 7X There is a 3.11% of reference with a coverageData >= 8X There is a 2.35% of reference with a coverageData >= 9X There is a 1.8% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.07% of reference with a coverageData >= 12X There is a 0.83% of reference with a coverageData >= 13X There is a 0.65% of reference with a coverageData >= 14X There is a 0.52% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 308488811 1.2376651651351351 4.578460371419705 chr2 243199373 319399125 1.3133221564678952 6.074481819436437 chr3 198022430 253828375 1.2818162821252117 2.8193073347357043 chr4 191154276 221596574 1.1592551243792213 2.8369949380586634 chr5 180915260 225078667 1.24411101086774 2.4958390521290696 chr6 171115067 213598014 1.2482712232465187 3.127039206585077 chr7 159138663 190185917 1.1950956066534253 2.7916377464169226 chr8 146364022 189554245 1.2950877026322767 2.930642248553463 chr9 141213431 162689963 1.1520856185414827 4.534646146132366 chr10 135534747 192473340 1.4201032890849754 19.00541608105242 chr11 135006516 178962369 1.3255831962955031 3.179834930230679 chr12 133851895 166085316 1.240814080368455 2.7529678453360034 chr13 115169878 110638873 0.9606580724171645 2.304402196730464 chr14 107349540 111982823 1.0431607159192298 2.408487948761291 chr15 102531392 111869887 1.091079374012595 2.5333625884188047 chr16 90354753 119414842 1.32162213978937 7.282810743874907 chr17 81195210 98434259 1.212316083670453 2.9413465927979012 chr18 78077248 91892838 1.1769477069683603 4.542528959488787 chr19 59128983 61655416 1.0427274894952954 3.116151745583983 chr20 63025520 90326242 1.433169325695369 2.982202655497671 chr21 48129895 47662116 0.9902809054538765 4.005986348929399 chr22 51304566 49181222 0.9586129624408088 2.494310546171598 chrMT 16571 40501 2.4440890712690844 2.6694804829953283 chrX 155270560 208098042 1.3402285790686914 2.7603086006826225 chrY 59373566 5643316 0.09504761765530471 2.4671933065848144