BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618625.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 29,787,784 number of mapped reads = 27,975,502 (93.92%) number of supplementary alignments = 151,628 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,290,215 number of mapped paired reads (second in pair) = 13,685,287 number of mapped paired reads (both in pair) = 26,973,422 number of mapped paired reads (singletons) = 1,002,080 number of mapped bases = 2,632,311,084 bp number of sequenced bases = 2,630,454,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,604,590 duplication rate = 17.44% >>>>>>> Insert size mean insert size = 136,824.0897 std insert size = 3,717,822.4237 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.2579 >>>>>>> ACTG content number of A's = 722,436,980 bp (27.46%) number of C's = 570,109,743 bp (21.67%) number of T's = 732,728,936 bp (27.86%) number of G's = 605,088,474 bp (23%) number of N's = 90,117 bp (0%) GC percentage = 44.68% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 33,622,676 number of insertions = 490,039 mapped reads with insertion percentage = 1.72% number of deletions = 1,353,525 mapped reads with deletion percentage = 4.71% homopolymer indels = 52.86% >>>>>>> Coverage mean coverageData = 0.8503X std coverageData = 3.6891X There is a 22.78% of reference with a coverageData >= 1X There is a 14.13% of reference with a coverageData >= 2X There is a 9.66% of reference with a coverageData >= 3X There is a 7.05% of reference with a coverageData >= 4X There is a 5.32% of reference with a coverageData >= 5X There is a 4.13% of reference with a coverageData >= 6X There is a 3.27% of reference with a coverageData >= 7X There is a 2.63% of reference with a coverageData >= 8X There is a 2.15% of reference with a coverageData >= 9X There is a 1.77% of reference with a coverageData >= 10X There is a 1.47% of reference with a coverageData >= 11X There is a 1.24% of reference with a coverageData >= 12X There is a 1.05% of reference with a coverageData >= 13X There is a 0.89% of reference with a coverageData >= 14X There is a 0.76% of reference with a coverageData >= 15X There is a 0.65% of reference with a coverageData >= 16X There is a 0.57% of reference with a coverageData >= 17X There is a 0.49% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% 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 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 230817729 0.9260467559677614 4.802959893260897 chr2 243199373 222946261 0.9167221866151768 4.659035995061465 chr3 198022430 170928537 0.8631776561877359 2.9771298363292513 chr4 191154276 135504115 0.7088730518379824 2.8115091622034254 chr5 180915260 148810888 0.8225446985511339 2.8823390169454295 chr6 171115067 145386929 0.8496442279977602 2.955031355956508 chr7 159138663 135342090 0.8504664262511744 3.204180490036802 chr8 146364022 127666661 0.8722543918614097 2.946180863472853 chr9 141213431 113531345 0.8039698787574958 3.7926115462399914 chr10 135534747 131751061 0.972083276917911 3.3712447811112365 chr11 135006516 130688712 0.9680178103403543 3.469796607643601 chr12 133851895 117440325 0.8773900810294841 3.340115478603652 chr13 115169878 71752196 0.6230118260609775 2.46754293616982 chr14 107349540 79649783 0.7419666912405959 2.7598740456965283 chr15 102531392 86513867 0.8437793080971728 3.335474095049137 chr16 90354753 90124204 0.9974484020779737 7.69143797196275 chr17 81195210 84317914 1.0384592145275564 3.8047138392366944 chr18 78077248 66300681 0.8491677498674134 3.778662311772813 chr19 59128983 54431425 0.9205540538385381 4.282842660711313 chr20 63025520 74057889 1.1750460607068376 3.6187152952821964 chr21 48129895 33289455 0.6916585835061556 4.160928821857431 chr22 51304566 44317873 0.8638192748770158 3.478145369252388 chrMT 16571 3690 0.22267817271136323 1.1766788959820866 chrX 155270560 132450566 0.8530307741531943 2.679832585649018 chrY 59373566 4286888 0.07220196273877166 2.6089696415151926