BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089757.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 = 18,765,791 number of mapped reads = 15,270,320 (81.37%) number of supplementary alignments = 781 (0%) number of secondary alignments = 0 number of mapped bases = 718,373,281 bp number of sequenced bases = 718,239,752 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,718,942 duplication rate = 12.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2339 >>>>>>> ACTG content number of A's = 210,445,240 bp (29.3%) number of C's = 147,325,135 bp (20.51%) number of T's = 206,180,966 bp (28.71%) number of G's = 154,274,369 bp (21.48%) number of N's = 14,042 bp (0%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 3,305,832 number of insertions = 27,013 mapped reads with insertion percentage = 0.18% number of deletions = 87,242 mapped reads with deletion percentage = 0.57% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.2321X std coverageData = 1.2718X There is a 11.64% of reference with a coverageData >= 1X There is a 4.99% of reference with a coverageData >= 2X There is a 2.54% of reference with a coverageData >= 3X There is a 1.41% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.32% 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 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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% 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 60852081 0.24414013796980671 1.9229554203156753 chr2 243199373 78316329 0.3220252093330849 1.4669407194932675 chr3 198022430 56800939 0.2868409351405293 0.9952843034356449 chr4 191154276 36278357 0.1897857466709246 0.8057026949125283 chr5 180915260 27538986 0.15222035996300146 0.6917559889174788 chr6 171115067 41529945 0.2427018597958998 0.9464126395509388 chr7 159138663 54091797 0.3399035531673406 2.378115944208979 chr8 146364022 62955839 0.4301319281865594 1.9870087369263438 chr9 141213431 23009721 0.16294286483273676 0.9778134401829803 chr10 135534747 22963786 0.16943098731722278 1.0795538243875382 chr11 135006516 27904247 0.20668814977789665 1.0265241772565488 chr12 133851895 28694454 0.21437465640662018 0.8533723628130928 chr13 115169878 22469139 0.1950956221382817 0.7909755703735645 chr14 107349540 24445253 0.2277164205827058 0.884980798228513 chr15 102531392 18248656 0.1779811591751334 0.7563237922161377 chr16 90354753 15853756 0.17546122891841673 0.8205885233402793 chr17 81195210 15608332 0.1922321772429679 0.8650312120810206 chr18 78077248 26412920 0.33829214882163877 1.767369547031647 chr19 59128983 13810353 0.23356317493233394 1.3244002836312467 chr20 63025520 18129064 0.28764640101343075 1.0404564991726974 chr21 48129895 10743800 0.2232250870275117 0.960870530775076 chr22 51304566 6161419 0.12009494437590604 0.6278693505630502 chrMT 16571 332763 20.081045199444812 14.728279588042696 chrX 155270560 23387389 0.15062346010731203 0.7658407599460013 chrY 59373566 1833956 0.0308884260042592 0.9581567565938665