BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818754.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,206,587 number of mapped reads = 1,176,920 (97.54%) number of supplementary alignments = 9,095 (0.75%) number of secondary alignments = 0 number of mapped bases = 80,063,354 bp number of sequenced bases = 80,030,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 498,305 duplication rate = 35.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.029 >>>>>>> ACTG content number of A's = 22,852,431 bp (28.55%) number of C's = 16,390,615 bp (20.48%) number of T's = 22,535,534 bp (28.16%) number of G's = 18,247,330 bp (22.8%) number of N's = 4,454 bp (0.01%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 389,079 number of insertions = 11,093 mapped reads with insertion percentage = 0.93% number of deletions = 20,608 mapped reads with deletion percentage = 1.73% homopolymer indels = 38.39% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.3432X There is a 1.31% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% 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 0.01% 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 6703699 0.02689541543810236 0.4405929884298616 chr2 243199373 6926544 0.028480928690552174 0.5048250950243942 chr3 198022430 5433348 0.027438043256008928 0.2925855418125973 chr4 191154276 5217512 0.02729477001079484 0.30812733447139423 chr5 180915260 5003033 0.027654013265658188 0.29768853011036095 chr6 171115067 4716152 0.027561290087914934 0.30923729594798643 chr7 159138663 4397930 0.02763583605072766 0.32611209356699145 chr8 146364022 4066629 0.027784348533412124 0.31463236567804886 chr9 141213431 3379209 0.023929798858863503 0.2947866237457242 chr10 135534747 3915688 0.02889065783256304 0.36961715544051027 chr11 135006516 3829376 0.028364379094117206 0.3103367296721278 chr12 133851895 3764820 0.028126759057090674 0.30842490370968834 chr13 115169878 2597464 0.022553327702578622 0.2647657133423175 chr14 107349540 2488870 0.023184729063580524 0.28412937666899135 chr15 102531392 2338915 0.02281169653875371 0.269147476304659 chr16 90354753 2381396 0.026356067842939042 0.39386597951327107 chr17 81195210 2310443 0.02845541011594157 0.3091949930952901 chr18 78077248 2115341 0.02709292468914888 0.35561284436524376 chr19 59128983 1574949 0.026635820879922795 0.39870830168260957 chr20 63025520 1737278 0.02756467538863622 0.30784055903915686 chr21 48129895 1134116 0.02356364999341885 0.28724181704198964 chr22 51304566 1034152 0.020157114281017404 0.2728109962630431 chrMT 16571 37490 2.262386096192143 3.6176633798484783 chrX 155270560 2266423 0.014596604791017691 0.22111271718748282 chrY 59373566 692577 0.011664736458645587 0.4494682824143878