BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080672.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,451,616 number of mapped reads = 1,289,492 (88.83%) number of supplementary alignments = 12,044 (0.83%) number of secondary alignments = 0 number of mapped bases = 84,605,858 bp number of sequenced bases = 84,574,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,628 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0433 >>>>>>> ACTG content number of A's = 22,429,024 bp (26.52%) number of C's = 15,882,185 bp (18.78%) number of T's = 26,525,001 bp (31.36%) number of G's = 19,735,022 bp (23.33%) number of N's = 3,683 bp (0%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 581,026 number of insertions = 6,177 mapped reads with insertion percentage = 0.48% number of deletions = 19,005 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2252X There is a 2.35% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 10589757 0.04248638160865405 0.2589203696468718 chr2 243199373 5897266 0.024248689160888584 0.3699388556329317 chr3 198022430 5427913 0.027410596870263638 0.1869625995794333 chr4 191154276 3655444 0.019123004080745753 0.15908838669374878 chr5 180915260 3974144 0.02196688106907068 0.16784120166498656 chr6 171115067 5150579 0.03010009048472628 0.2355888713001594 chr7 159138663 5358769 0.03367358314427965 0.3346592180732476 chr8 146364022 10140937 0.06928572241612764 0.3193644331755863 chr9 141213431 2759088 0.01953842478340463 0.16849692768203056 chr10 135534747 4027719 0.029717242914837183 0.20278578516086232 chr11 135006516 3546571 0.026269628348901324 0.18960945914378127 chr12 133851895 2710691 0.020251420422549862 0.16043593826852598 chr13 115169878 1697243 0.01473686548491438 0.13812477161928557 chr14 107349540 1729638 0.016112206908385447 0.1447024445686761 chr15 102531392 1533850 0.014959808601837767 0.15005301279840405 chr16 90354753 2355741 0.026072131479347855 0.18592001950505574 chr17 81195210 1543091 0.01900470483418911 0.1560432977706759 chr18 78077248 2065198 0.026450701746045146 0.21877158419627887 chr19 59128983 1597045 0.027009512407815302 0.20002354451866977 chr20 63025520 2292817 0.03637918417809167 0.21870930608508585 chr21 48129895 1269479 0.026376101589251338 0.18597148040621508 chr22 51304566 919047 0.017913551787963666 0.1522812903602754 chrMT 16571 10240 0.6179470158711001 0.8741473755327106 chrX 155270560 4200541 0.027053042122086764 0.18955658272909226 chrY 59373566 153050 0.002577746467173624 0.05726416807968229