BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080647.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 = 1,419,294 number of mapped reads = 1,277,790 (90.03%) number of supplementary alignments = 12,511 (0.88%) number of secondary alignments = 0 number of mapped bases = 84,163,456 bp number of sequenced bases = 84,132,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,782 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2927 >>>>>>> ACTG content number of A's = 22,665,953 bp (26.94%) number of C's = 15,574,245 bp (18.51%) number of T's = 26,603,619 bp (31.62%) number of G's = 19,284,815 bp (22.92%) number of N's = 3,557 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 576,020 number of insertions = 6,382 mapped reads with insertion percentage = 0.5% number of deletions = 19,413 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2202X There is a 2.33% 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 10079511 0.04043926133287347 0.2576792790788024 chr2 243199373 5733921 0.02357703858060522 0.3259663936472915 chr3 198022430 5197070 0.026244855191404327 0.183844562159284 chr4 191154276 3310874 0.017320428657321797 0.1518611257832566 chr5 180915260 3863551 0.021355583824161653 0.166002098320065 chr6 171115067 5204512 0.03041527605514715 0.22633447760233746 chr7 159138663 5244210 0.03295371408266764 0.33338843384625205 chr8 146364022 10227465 0.06987690595165524 0.32535000355710547 chr9 141213431 2687911 0.019034386325476365 0.16913638535669961 chr10 135534747 3936253 0.029042390140736382 0.20062997236643645 chr11 135006516 3394018 0.025139660666452575 0.19194280157515078 chr12 133851895 2779889 0.020768394799341467 0.16405807122158828 chr13 115169878 1735942 0.015072882164553478 0.1395984344512826 chr14 107349540 1623053 0.015119328876490762 0.14044739509234824 chr15 102531392 1550676 0.015123914439784452 0.1480674279794917 chr16 90354753 2157834 0.023881798448389318 0.17844484162970933 chr17 81195210 1402512 0.01727333422747475 0.15060764790303544 chr18 78077248 2653498 0.033985547236500956 0.2353451554495538 chr19 59128983 1300116 0.021987795731240635 0.18618779459090387 chr20 63025520 2030943 0.03222413714317629 0.2068791414382234 chr21 48129895 1240344 0.02577076056367877 0.18481815236855337 chr22 51304566 799056 0.015574754106681264 0.14005347975042115 chrMT 16571 3694 0.22291955826443788 0.5058335092971359 chrX 155270560 5832286 0.037562085175708776 0.22494859788223026 chrY 59373566 174317 0.0029359361706521045 0.062405746301385207