BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046492.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,903,854 number of mapped reads = 7,725,388 (97.74%) number of supplementary alignments = 50,702 (0.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,940,322 number of mapped paired reads (second in pair) = 3,785,066 number of mapped paired reads (both in pair) = 7,560,758 number of mapped paired reads (singletons) = 164,630 number of mapped bases = 748,852,295 bp number of sequenced bases = 748,657,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,375,593 duplication rate = 35.76% >>>>>>> Insert size mean insert size = 37,193.2953 std insert size = 1,862,617.8944 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 52.9798 >>>>>>> ACTG content number of A's = 223,047,793 bp (29.79%) number of C's = 151,688,567 bp (20.26%) number of T's = 223,323,616 bp (29.83%) number of G's = 150,539,047 bp (20.11%) number of N's = 58,842 bp (0.01%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 3,382,399 number of insertions = 61,683 mapped reads with insertion percentage = 0.78% number of deletions = 70,471 mapped reads with deletion percentage = 0.88% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 0.2419X std coverageData = 18.918X There is a 3.18% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 102068742 0.4095024581704051 22.06517128594687 chr2 243199373 61711232 0.25374749629802706 17.210503729925108 chr3 198022430 22912564 0.11570691259570949 5.502662699250935 chr4 191154276 26001165 0.13602188527553524 13.064121739488442 chr5 180915260 83714472 0.46272753332140143 38.5088027498084 chr6 171115067 54359530 0.3176782205859172 17.656627072166398 chr7 159138663 24066417 0.1512292270546473 7.420837594272475 chr8 146364022 113445395 0.7750907186740195 40.31959994062061 chr9 141213431 10032637 0.07104591205633974 2.9725205696236303 chr10 135534747 39196733 0.28920062100385224 27.4124760548723 chr11 135006516 13156225 0.09744881498904838 4.433026179840242 chr12 133851895 19116384 0.14281743265569755 7.3141135482276844 chr13 115169878 20775148 0.18038699320320545 12.25172665613182 chr14 107349540 51821861 0.482739478902285 33.448139906228015 chr15 102531392 11229730 0.10952479802478444 4.171482267895508 chr16 90354753 18990850 0.21018097409883904 10.565545645537565 chr17 81195210 33616637 0.41402241585433425 17.097711418144826 chr18 78077248 10768380 0.13791956396823823 8.480245053097839 chr19 59128983 2421536 0.040953452556422285 2.3560007719250704 chr20 63025520 12826337 0.20351021300577923 12.571399524507006 chr21 48129895 2234753 0.04643170320649983 3.514738343776673 chr22 51304566 2237805 0.04361804756325197 2.7124477141683343 chrMT 16571 61805 3.729708526944662 2.557466063520201 chrX 155270560 11911814 0.07671650053944547 5.4977378168628555 chrY 59373566 174143 0.002933005573557768 0.27968219137208644