BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089731.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 16,993,432 number of mapped reads = 14,636,337 (86.13%) number of supplementary alignments = 80,052 (0.47%) number of secondary alignments = 0 number of mapped bases = 945,861,588 bp number of sequenced bases = 945,552,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,490,827 duplication rate = 16.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5652 >>>>>>> ACTG content number of A's = 245,061,744 bp (25.92%) number of C's = 176,079,495 bp (18.62%) number of T's = 296,191,386 bp (31.32%) number of G's = 227,827,085 bp (24.09%) number of N's = 392,367 bp (0.04%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 6,293,440 number of insertions = 62,640 mapped reads with insertion percentage = 0.42% number of deletions = 176,395 mapped reads with deletion percentage = 1.19% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.3055X std coverageData = 2.4515X There is a 9.6% of reference with a coverageData >= 1X There is a 5.73% of reference with a coverageData >= 2X There is a 3.84% of reference with a coverageData >= 3X There is a 2.7% of reference with a coverageData >= 4X There is a 1.95% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 1.07% of reference with a coverageData >= 7X There is a 0.8% of reference with a coverageData >= 8X There is a 0.61% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% 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% 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 73634487 0.29542348462192997 4.541499476210506 chr2 243199373 80621735 0.33150469923292114 3.769440735155819 chr3 198022430 67467376 0.3407057271239425 1.454316556140605 chr4 191154276 62176487 0.3252686170619589 1.827081141541319 chr5 180915260 58266280 0.3220639320309409 1.4345920777332175 chr6 171115067 55076322 0.32186716789819564 1.6726244137350688 chr7 159138663 51581207 0.3241274372149275 2.900428653760926 chr8 146364022 47531980 0.3247518027346912 2.7138832202781793 chr9 141213431 40660916 0.2879394382819011 2.188216487177643 chr10 135534747 45140960 0.3330582083131789 2.375839999408918 chr11 135006516 44758863 0.33153113143072294 1.8734631295639106 chr12 133851895 42851272 0.3201394496506755 1.5489852155290589 chr13 115169878 30209619 0.26230486238771566 1.2845375627055107 chr14 107349540 29010624 0.270244511527483 1.3942783471490907 chr15 102531392 24844902 0.24231507556241896 1.3560378873941048 chr16 90354753 26570015 0.2940632796594552 1.4762428886318484 chr17 81195210 24205574 0.298115787864826 1.6764478544240549 chr18 78077248 25364280 0.32486134757208657 3.2793420950650605 chr19 59128983 17610594 0.29783353452908196 2.99916236869075 chr20 63025520 18720142 0.2970247924967537 1.5472356495655752 chr21 48129895 12436042 0.2583849808938914 1.612902802308705 chr22 51304566 10807453 0.21065284910508744 1.2195119521613542 chrMT 16571 754451 45.528392975680404 30.79126434717122 chrX 155270560 52364790 0.3372486709650561 1.6876056096502072 chrY 59373566 3195217 0.05381548078146426 1.8963350603213545