BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082959.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 = 3,122,048 number of mapped reads = 2,580,181 (82.64%) number of supplementary alignments = 14,037 (0.45%) number of secondary alignments = 0 number of mapped bases = 174,250,181 bp number of sequenced bases = 174,172,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,937 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3141 >>>>>>> ACTG content number of A's = 48,870,620 bp (28.06%) number of C's = 31,530,919 bp (18.1%) number of T's = 56,371,362 bp (32.37%) number of G's = 37,382,634 bp (21.46%) number of N's = 17,317 bp (0.01%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,618,485 number of insertions = 16,441 mapped reads with insertion percentage = 0.63% number of deletions = 43,748 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0563X std coverageData = 0.5003X There is a 4.65% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% 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 0.01% 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 13875552 0.05566907694885944 0.9587852422060937 chr2 243199373 14958694 0.06150794640412169 0.5567512199282958 chr3 198022430 11504488 0.058096893367079676 0.28424027283007897 chr4 191154276 12681261 0.06634045162557599 0.32893252466828543 chr5 180915260 10422605 0.05761042490279703 0.2838524979449582 chr6 171115067 12552686 0.07335815729189996 0.4063053115116016 chr7 159138663 10644858 0.06689045766332723 0.6230944710861474 chr8 146364022 8547213 0.058396953590138426 0.7175101355958786 chr9 141213431 8760976 0.06204067090473852 0.505300195545543 chr10 135534747 7468205 0.05510177401223909 0.417553549418853 chr11 135006516 6493166 0.048095204530720574 0.34380032857180326 chr12 133851895 6462081 0.04827784470290839 0.2703986718861885 chr13 115169878 5214680 0.045278158582402944 0.24779313239609282 chr14 107349540 4516393 0.04207184306518687 0.29006161881302245 chr15 102531392 4680875 0.04565309129910184 0.24859193626827703 chr16 90354753 4862330 0.053813771147158136 0.3716186697757149 chr17 81195210 4473490 0.05509549147049438 0.3137902851470648 chr18 78077248 4738272 0.06068697503272656 0.9257099254787824 chr19 59128983 3459629 0.05850986816397637 0.6579025738590113 chr20 63025520 3612895 0.0573243187838831 0.29655438313733956 chr21 48129895 2340411 0.048626970825512913 0.3020148003037078 chr22 51304566 1896925 0.0369738046317359 0.2238895982024873 chrMT 16571 13640 0.8231247359845513 1.0234253459134424 chrX 155270560 9580644 0.06170290105220204 0.32038223657850523 chrY 59373566 488212 0.008222716486323223 0.2622507031550281