BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 25,423,480 number of mapped reads = 18,593,645 (73.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,325,852 number of mapped paired reads (second in pair) = 9,267,793 number of mapped paired reads (both in pair) = 16,668,012 number of mapped paired reads (singletons) = 1,925,633 number of mapped bases = 718,239,132 bp number of sequenced bases = 718,155,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,110,695 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 70,466.9328 std insert size = 2,566,275.444 median insert size = 90 >>>>>>> Mapping quality mean mapping quality = 47.1436 >>>>>>> ACTG content number of A's = 205,295,746 bp (28.59%) number of C's = 151,776,313 bp (21.13%) number of T's = 206,255,337 bp (28.72%) number of G's = 154,743,195 bp (21.55%) number of N's = 85,288 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 4,096,055 number of insertions = 21,688 mapped reads with insertion percentage = 0.12% number of deletions = 64,264 mapped reads with deletion percentage = 0.35% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.232X std coverageData = 1.0678X There is a 14.27% of reference with a coverageData >= 1X There is a 5.22% of reference with a coverageData >= 2X There is a 1.94% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 59129771 0.23723018527604792 1.3859479227832292 chr2 243199373 60867865 0.25027969541681344 0.9728334290736487 chr3 198022430 49494127 0.24994202424442524 0.7224962656838403 chr4 191154276 47578154 0.24889923989981788 0.8796500946619008 chr5 180915260 43513163 0.24051681986362014 0.7121675514510559 chr6 171115067 42257323 0.24695267191170256 1.0500068959737487 chr7 159138663 38657492 0.24291703393285388 1.3529878650127791 chr8 146364022 36115316 0.24674995607868716 2.4681295232758207 chr9 141213431 29329533 0.20769648320491554 0.7908252548675098 chr10 135534747 33436825 0.2467029727808471 1.1461400615779354 chr11 135006516 32982101 0.2443000677093245 0.8122726856195781 chr12 133851895 32276442 0.2411354878464739 0.7180336409343949 chr13 115169878 23434273 0.20347571263381906 0.6584472324678906 chr14 107349540 22526856 0.20984585495196345 0.7103592203865033 chr15 102531392 20611703 0.20102821777743932 0.6546749629009354 chr16 90354753 20570061 0.22765887036401947 0.8209124182488268 chr17 81195210 18800700 0.2315493734174713 0.7561293132951373 chr18 78077248 18728436 0.23987059584887008 1.193618332517306 chr19 59128983 13810517 0.23356594852984364 1.3209472970326148 chr20 63025520 15357232 0.24366688287538127 0.7676929534334601 chr21 48129895 9415717 0.19563136383322674 0.7641931207249092 chr22 51304566 7954668 0.15504795421132692 0.6340353743449092 chrMT 16571 42440 2.5611007181220202 2.5601375286553454 chrX 155270560 39521130 0.25453073654142805 0.8019581186146315 chrY 59373566 1827287 0.030776103291488336 0.6158387524430758