BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084842.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 = 2,564,133 number of mapped reads = 2,330,795 (90.9%) number of supplementary alignments = 21,709 (0.85%) number of secondary alignments = 0 number of mapped bases = 162,660,039 bp number of sequenced bases = 162,597,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,899 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.4247 >>>>>>> ACTG content number of A's = 47,634,941 bp (29.3%) number of C's = 29,877,947 bp (18.38%) number of T's = 52,231,932 bp (32.12%) number of G's = 32,826,302 bp (20.19%) number of N's = 25,945 bp (0.02%) GC percentage = 38.56% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,338,433 number of insertions = 13,052 mapped reads with insertion percentage = 0.55% number of deletions = 35,629 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0525X std coverageData = 0.4637X There is a 4.09% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% 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 12961997 0.052003870433686906 0.6819937213065177 chr2 243199373 13651561 0.0561332080407954 0.37525379016451454 chr3 198022430 11423317 0.05768698525717516 0.293463342439089 chr4 191154276 11089582 0.05801377940402442 0.304417988127176 chr5 180915260 10379586 0.05737263954406057 0.294127390810746 chr6 171115067 9781249 0.05716182199198157 0.2980493762767292 chr7 159138663 8528994 0.053594732035671305 0.32231011308767654 chr8 146364022 9673962 0.06609521840005189 1.3023148773685964 chr9 141213431 6520193 0.04617261229209848 0.3697071575582938 chr10 135534747 7564716 0.05581384971338752 0.3417449508777278 chr11 135006516 7554995 0.05596022491240349 0.33496834144944215 chr12 133851895 7640274 0.05708005852289204 0.294649838890927 chr13 115169878 5306392 0.04607447791166367 0.26296997912437564 chr14 107349540 4842443 0.045109117374885814 0.2726128464559836 chr15 102531392 4829209 0.04709980919794788 0.2643536103008394 chr16 90354753 4072936 0.045077163787941514 0.27649733106834634 chr17 81195210 3383147 0.04166682985363299 0.30800314573467197 chr18 78077248 4444945 0.05693009313033164 0.6764833281989864 chr19 59128983 2347689 0.039704538804599426 0.4733851612136971 chr20 63025520 3008546 0.04773536180264756 0.27403553559642546 chr21 48129895 2006778 0.04169504213545448 0.26004528460700205 chr22 51304566 1422694 0.027730358346662556 0.19878014615032322 chrMT 16571 354345 21.38344095105908 11.060537016197918 chrX 155270560 9513509 0.06127052675020944 0.31787367770945474 chrY 59373566 356980 0.006012439946760146 0.13161984147281897