BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238266.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,352,737 number of mapped reads = 1,173,445 (86.75%) number of supplementary alignments = 13,888 (1.03%) number of secondary alignments = 0 number of mapped bases = 75,390,626 bp number of sequenced bases = 75,347,205 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,109 duplication rate = 5.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1228 >>>>>>> ACTG content number of A's = 21,142,364 bp (28.06%) number of C's = 14,290,462 bp (18.97%) number of T's = 23,366,782 bp (31.01%) number of G's = 16,530,491 bp (21.94%) number of N's = 17,106 bp (0.02%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 692,345 number of insertions = 6,042 mapped reads with insertion percentage = 0.51% number of deletions = 26,373 mapped reads with deletion percentage = 2.22% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2666X There is a 1.79% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6503577 0.026092520748423734 0.4365262721915444 chr2 243199373 5766785 0.02371217050793959 0.32003379983568875 chr3 198022430 4833968 0.024411214426567737 0.20104913376102768 chr4 191154276 3333333 0.01743792014362263 0.1751618642600322 chr5 180915260 3904391 0.021581324869997146 0.19048633308979812 chr6 171115067 3899877 0.022790962060634905 0.20921943614595934 chr7 159138663 3899158 0.024501638549018098 0.2986410390941752 chr8 146364022 5101168 0.0348526087920705 0.3570057223286958 chr9 141213431 2376340 0.016828002713141357 0.21228530151120684 chr10 135534747 4313692 0.031827203691168586 0.3004736145627133 chr11 135006516 2797976 0.02072474783365271 0.2457990388145648 chr12 133851895 6001717 0.044838491080010486 0.27857617666639567 chr13 115169878 1703033 0.014787139046895577 0.15886271704829738 chr14 107349540 2921683 0.027216539539899286 0.22840945571065246 chr15 102531392 2110887 0.020587714248529856 0.2169272924114144 chr16 90354753 3640787 0.040294360607681594 0.2628215352185876 chr17 81195210 1882278 0.023182131064135435 0.22061368875719495 chr18 78077248 2340337 0.029974634864179638 0.31904315953632983 chr19 59128983 1108151 0.018741249109594866 0.2810727998868242 chr20 63025520 1061475 0.016841987182335028 0.16746433153645435 chr21 48129895 1591787 0.03307272953743198 0.24019662766476052 chr22 51304566 667137 0.013003462498834899 0.14367879160246352 chrMT 16571 8823 0.5324361836944059 0.916716915253408 chrX 155270560 3441581 0.022165058205496264 0.21499483359977734 chrY 59373566 180685 0.0030431892873000084 0.09854033196538999