BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 4,594,787 number of mapped reads = 3,869,558 (84.22%) number of secondary alignments = 0 number of mapped bases = 152,906,695 bp number of sequenced bases = 152,893,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,155 duplication rate = 2.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.5929 >>>>>>> ACTG content number of A's = 41,984,241 bp (27.46%) number of C's = 33,810,074 bp (22.11%) number of T's = 43,177,111 bp (28.24%) number of G's = 33,920,539 bp (22.19%) number of N's = 1,169 bp (0%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 444,044 number of insertions = 4,944 mapped reads with insertion percentage = 0.13% number of deletions = 10,626 mapped reads with deletion percentage = 0.27% homopolymer indels = 38.79% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.3685X There is a 4.2% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 12578113 0.05046371780152957 0.47747285726344146 chr2 243199373 13010400 0.05349684844787819 0.3753167336569478 chr3 198022430 10167705 0.051346228808524366 0.2605035201033291 chr4 191154276 10129743 0.052992500152076114 0.27741239949197966 chr5 180915260 9335190 0.05159979318494194 0.2621640420075635 chr6 171115067 9110284 0.053240688618028005 0.27178097237372734 chr7 159138663 8468167 0.053212505624733064 0.40397277681885363 chr8 146364022 7840158 0.053566155759234325 0.803640180638942 chr9 141213431 6451645 0.045687191043463846 0.36690505600685436 chr10 135534747 7081606 0.05224937631676104 0.3191819457207876 chr11 135006516 6982440 0.05171928146045929 0.29019285620471647 chr12 133851895 7107294 0.053098194836912846 0.2664612013312333 chr13 115169878 4987792 0.04330812957881226 0.23836163602960306 chr14 107349540 4774541 0.04447658555406944 0.27497829917627326 chr15 102531392 4396758 0.04288206679179778 0.23746666383594595 chr16 90354753 4619067 0.05112146120304263 0.2798530668242547 chr17 81195210 4493206 0.055338313676385587 0.27648933974057394 chr18 78077248 3971596 0.0508675203306346 0.59618022859877 chr19 59128983 3500366 0.05919881963807833 0.5037099647571707 chr20 63025520 3187524 0.05057513210521706 0.2625521475019392 chr21 48129895 1887384 0.03921438016850026 0.27026812397808603 chr22 51304566 1935862 0.03773274292974235 0.29365282362778605 chrMT 16571 2229 0.13451209945084786 0.42443418873116273 chrX 155270560 5553822 0.03576867372668715 0.25336640852330583 chrY 59373566 1333803 0.022464593081709124 0.22748606526831147