BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549027.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 = 5,838,100 number of mapped reads = 5,148,102 (88.18%) number of secondary alignments = 0 number of mapped bases = 203,868,275 bp number of sequenced bases = 203,847,736 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,485 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.852 >>>>>>> ACTG content number of A's = 58,258,670 bp (28.58%) number of C's = 43,232,332 bp (21.21%) number of T's = 58,740,712 bp (28.82%) number of G's = 43,613,822 bp (21.4%) number of N's = 2,200 bp (0%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 555,772 number of insertions = 6,319 mapped reads with insertion percentage = 0.12% number of deletions = 15,810 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.95% >>>>>>> Coverage mean coverageData = 0.0659X std coverageData = 0.5535X There is a 5.37% of reference with a coverageData >= 1X There is a 0.9% 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 16144388 0.06477170622575901 0.5183596971637938 chr2 243199373 17215116 0.07078602131100066 0.40393111434089385 chr3 198022430 13587891 0.06861793888702405 0.30949991251362197 chr4 191154276 12795464 0.06693789052356851 0.31058041362730127 chr5 180915260 12637483 0.06985305164417861 0.3145555133716069 chr6 171115067 12029905 0.07030301428687165 0.3317548957572175 chr7 159138663 11205633 0.07041427135780323 0.5575609399947181 chr8 146364022 10368415 0.0708399158366938 1.8600628288695535 chr9 141213431 8589561 0.06082679911657978 0.39868633251360774 chr10 135534747 9525209 0.07027872343318721 0.3498218837484299 chr11 135006516 9311260 0.06896896739413674 0.46160520227440166 chr12 133851895 9262117 0.0691967566092359 0.3159257305490285 chr13 115169878 6571860 0.05706231624209934 0.2811681785769093 chr14 107349540 6052909 0.05638504831972266 0.31517121335981413 chr15 102531392 5976009 0.05828467636526382 0.28541161917974117 chr16 90354753 5689957 0.06297352171390475 0.3139472018971217 chr17 81195210 5704375 0.07025506800216416 0.3327609434947159 chr18 78077248 5439469 0.06966778593425833 0.6317315180586871 chr19 59128983 4266007 0.07214747799738075 0.5172106294532286 chr20 63025520 4228575 0.06709306008105922 0.31394929476593547 chr21 48129895 2555556 0.05309706160796736 0.30397418850494257 chr22 51304566 2409919 0.04697279770381451 0.28472327761932803 chrMT 16571 7179 0.4332267213807254 0.7884288306199457 chrX 155270560 11692423 0.07530354112202596 0.3709735670369982 chrY 59373566 601595 0.010132371028548293 0.14026333289854764