BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083615.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 = 1,609,630 number of mapped reads = 1,448,814 (90.01%) number of supplementary alignments = 12,032 (0.75%) number of secondary alignments = 0 number of mapped bases = 96,646,788 bp number of sequenced bases = 96,611,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,082 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6351 >>>>>>> ACTG content number of A's = 26,059,440 bp (26.97%) number of C's = 18,306,208 bp (18.95%) number of T's = 30,022,294 bp (31.08%) number of G's = 22,218,892 bp (23%) number of N's = 4,391 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 654,045 number of insertions = 6,800 mapped reads with insertion percentage = 0.47% number of deletions = 21,938 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.2598X There is a 2.67% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 10005785 0.04014347069570591 0.4197251671941563 chr2 243199373 9319621 0.03832090882898781 0.37570870880941715 chr3 198022430 8108434 0.04094704827124887 0.234056951962098 chr4 191154276 4746199 0.024829154227237898 0.18177467909714928 chr5 180915260 4735859 0.026177222418938016 0.18433961876541288 chr6 171115067 6963497 0.04069482087161851 0.2785315094802941 chr7 159138663 6575255 0.04131777203632784 0.36478009042729104 chr8 146364022 5696495 0.03892004962804316 0.2526421455495298 chr9 141213431 3409277 0.024142724780902746 0.19612433105088492 chr10 135534747 4026157 0.029705718194906874 0.21332769423920417 chr11 135006516 3658336 0.02709747728028179 0.2169314468228728 chr12 133851895 3340739 0.024958473692135625 0.17955058697275322 chr13 115169878 3439728 0.029866559379354382 0.19709820814391318 chr14 107349540 1794655 0.01671786390514575 0.14847792195125553 chr15 102531392 2373838 0.02315230441814347 0.17961975921047635 chr16 90354753 2471535 0.02735367999954579 0.19150063458140926 chr17 81195210 1920980 0.02365878479777317 0.18074847624216023 chr18 78077248 2887948 0.036988342621912085 0.2982208029609919 chr19 59128983 2822140 0.0477285394879868 0.33122842822043574 chr20 63025520 2045431 0.032454012279470285 0.20912038376106654 chr21 48129895 1573558 0.032693983645715415 0.21027802064590861 chr22 51304566 808422 0.015757310957469167 0.14449216348128444 chrMT 16571 3545 0.21392794641240723 0.5046603673642576 chrX 155270560 3767056 0.024261237932032963 0.1861876104422305 chrY 59373566 152298 0.0025650808981222384 0.06386402457021512