BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006036.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 = 12,759,904 number of mapped reads = 9,553,874 (74.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,793,412 number of mapped paired reads (second in pair) = 4,760,462 number of mapped paired reads (both in pair) = 8,554,190 number of mapped paired reads (singletons) = 999,684 number of mapped bases = 369,321,946 bp number of sequenced bases = 369,278,359 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 350,137 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 70,384.6851 std insert size = 2,523,774.3985 median insert size = 101 >>>>>>> Mapping quality mean mapping quality = 47.4227 >>>>>>> ACTG content number of A's = 106,788,088 bp (28.92%) number of C's = 76,949,074 bp (20.84%) number of T's = 107,236,779 bp (29.04%) number of G's = 78,259,250 bp (21.19%) number of N's = 45,168 bp (0.01%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 2,088,057 number of insertions = 10,746 mapped reads with insertion percentage = 0.11% number of deletions = 33,531 mapped reads with deletion percentage = 0.35% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.1193X std coverageData = 0.6086X There is a 8.85% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 30006153 0.1203854693706059 0.8262958444026876 chr2 243199373 31287123 0.12864804137467903 0.5541326679266232 chr3 198022430 25725873 0.12991393449721833 0.45365163810681797 chr4 191154276 24638032 0.12889082324268802 0.5053179053621287 chr5 180915260 22820035 0.12613659566362728 0.4470714779234785 chr6 171115067 21997843 0.1285558506662654 0.5590697085338147 chr7 159138663 20000594 0.12568029429780994 0.7133585307449747 chr8 146364022 18956191 0.1295140072059512 1.3194490153059255 chr9 141213431 15257496 0.10804564333544166 0.4641902722279681 chr10 135534747 16976817 0.12525804176253047 0.6891183437876313 chr11 135006516 16150072 0.11962438909244943 0.4808219163496112 chr12 133851895 16636200 0.12428811710136789 0.4479958813733044 chr13 115169878 12116714 0.10520731818436067 0.4071764342996306 chr14 107349540 11140885 0.10378139487137067 0.42724508914416015 chr15 102531392 10797708 0.10531123970305602 0.40896578995837984 chr16 90354753 10257978 0.11353003200617459 0.4914094062701402 chr17 81195210 9382936 0.11556021592899383 0.4446245699707641 chr18 78077248 9929427 0.12717439784762904 0.68090593297616 chr19 59128983 6889014 0.11650824435793188 0.7038315720082574 chr20 63025520 7666110 0.12163501388009175 0.4582994917051984 chr21 48129895 4841661 0.10059571083626923 0.4424995416414661 chr22 51304566 4152589 0.08093994986723015 0.36466697818911314 chrMT 16571 69487 4.193289481624525 3.8788469549708537 chrX 155270560 20709162 0.13337468480824696 0.48979676357210117 chrY 59373566 915846 0.015425147278504378 0.32594668873371013