BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084805.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 = 1,908,861 number of mapped reads = 1,753,032 (91.84%) number of supplementary alignments = 19,114 (1%) number of secondary alignments = 0 number of mapped bases = 118,209,925 bp number of sequenced bases = 118,164,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,031 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8828 >>>>>>> ACTG content number of A's = 32,815,430 bp (27.77%) number of C's = 21,951,570 bp (18.58%) number of T's = 37,336,553 bp (31.6%) number of G's = 26,044,248 bp (22.04%) number of N's = 16,637 bp (0.01%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 875,325 number of insertions = 9,103 mapped reads with insertion percentage = 0.51% number of deletions = 27,321 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.2644X There is a 3.21% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9657284 0.03874527558348591 0.30789770224882174 chr2 243199373 9142323 0.03759188556789577 0.3762355681591315 chr3 198022430 9102395 0.04596648470579823 0.24789398409069427 chr4 191154276 8215078 0.042976166538905985 0.24358035985190776 chr5 180915260 5668360 0.03133157479363543 0.20647132771070947 chr6 171115067 5555812 0.03246828054013502 0.21950224883802638 chr7 159138663 6019662 0.037826521138989336 0.25518965542713884 chr8 146364022 6904585 0.047174058936423596 0.3068264287469543 chr9 141213431 8004657 0.05668481350049486 0.32846994990607215 chr10 135534747 3221917 0.02377188928533581 0.18446859603904453 chr11 135006516 4879715 0.036144292472520365 0.2421779107952853 chr12 133851895 4642155 0.03468127963373249 0.216460989486201 chr13 115169878 2964918 0.02574386681211905 0.1862599732667601 chr14 107349540 2342830 0.02182431335988957 0.17495874140997342 chr15 102531392 3066408 0.029907016184857804 0.20591373921413966 chr16 90354753 1778613 0.019684775188306917 0.167804286862609 chr17 81195210 2688685 0.033113837626628465 0.2109329598069599 chr18 78077248 4824032 0.061785374402540415 0.4158665927281417 chr19 59128983 2246512 0.03799341517509273 0.26517393420535934 chr20 63025520 2411890 0.03826846648786079 0.22713555202089872 chr21 48129895 1102808 0.02291316031335618 0.17949763949083564 chr22 51304566 1163530 0.022678878133380955 0.17142611181997086 chrMT 16571 30928 1.866393096373182 1.667608446510998 chrX 155270560 12249181 0.07888926915701212 0.3379598104227838 chrY 59373566 325647 0.005484713517123091 0.09205707597748339