BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506334.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 7,764,653 number of mapped reads = 4,507,537 (58.05%) number of supplementary alignments = 68,897 (0.89%) number of secondary alignments = 0 number of mapped bases = 341,721,047 bp number of sequenced bases = 341,582,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 450,035 duplication rate = 7.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2282 >>>>>>> ACTG content number of A's = 95,944,500 bp (28.09%) number of C's = 64,662,875 bp (18.93%) number of T's = 97,493,013 bp (28.54%) number of G's = 83,394,125 bp (24.41%) number of N's = 88,476 bp (0.03%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,409,040 number of insertions = 27,189 mapped reads with insertion percentage = 0.59% number of deletions = 69,483 mapped reads with deletion percentage = 1.51% homopolymer indels = 43.6% >>>>>>> Coverage mean coverageData = 0.1104X std coverageData = 0.7389X There is a 7.48% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 25396654 0.10189203901722677 1.1469375846913719 chr2 243199373 27220770 0.1119277967875353 0.8223183052525794 chr3 198022430 21871817 0.11045120999676653 0.46690648085210856 chr4 191154276 20936360 0.10952598308603884 0.6657003330081591 chr5 180915260 25894549 0.14313081715715967 0.5357387791882195 chr6 171115067 12224408 0.07143969385232453 0.39104906475957585 chr7 159138663 17233825 0.10829439355035929 0.947242667879982 chr8 146364022 21932936 0.14985196293662933 1.015015209647804 chr9 141213431 9626232 0.06816796342835123 0.6731761690185902 chr10 135534747 19136231 0.14119059077890928 0.8839113382119387 chr11 135006516 15125469 0.11203510355011309 0.7204467532363931 chr12 133851895 14712703 0.10991777890032861 0.5179187000354679 chr13 115169878 7336493 0.0637014914611614 0.34386383963270045 chr14 107349540 10250316 0.09548542080385254 0.4985617419680213 chr15 102531392 12671363 0.1235852040319515 0.510612738111449 chr16 90354753 12586474 0.13930062981855532 0.6234060623940673 chr17 81195210 8555446 0.10536885119208386 0.545405060597121 chr18 78077248 6126566 0.07846800645432585 1.1364542042177699 chr19 59128983 8216664 0.13896170005156355 0.9497136600436002 chr20 63025520 9142733 0.1450639836053713 0.5791348389772567 chr21 48129895 5616966 0.11670430612823901 0.6001918000961253 chr22 51304566 3880087 0.07562849279340945 0.3933729188814351 chrMT 16571 19239 1.1610041639007906 1.89602210414475 chrX 155270560 24781151 0.15959980436729282 0.6465954133829998 chrY 59373566 1225595 0.02064209853927251 0.6856596245767361