BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081096.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 = 2,566,998 number of mapped reads = 2,332,120 (90.85%) number of supplementary alignments = 26,695 (1.04%) number of secondary alignments = 0 number of mapped bases = 156,290,743 bp number of sequenced bases = 156,234,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,603 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5923 >>>>>>> ACTG content number of A's = 43,592,256 bp (27.9%) number of C's = 29,757,904 bp (19.05%) number of T's = 48,589,884 bp (31.1%) number of G's = 34,292,474 bp (21.95%) number of N's = 1,712 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,428,947 number of insertions = 12,308 mapped reads with insertion percentage = 0.52% number of deletions = 34,500 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.0505X std coverageData = 0.4009X There is a 4.2% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 13313378 0.0534136201811108 0.6220389063051258 chr2 243199373 10791078 0.04437132327639677 0.44035169376326433 chr3 198022430 12933770 0.06531467167633485 0.296835703355208 chr4 191154276 9124697 0.0477347260596985 0.2747976896657903 chr5 180915260 8646734 0.04779438727280385 0.25388728926687965 chr6 171115067 12565911 0.07343544446614979 0.4478856409042411 chr7 159138663 8187918 0.05145146908768487 0.45842076249079333 chr8 146364022 11560085 0.07898173910525634 0.4597980998356492 chr9 141213431 7937425 0.05620871147872613 0.49260098450645656 chr10 135534747 7679216 0.05665865152646059 0.40964229872559543 chr11 135006516 7144247 0.05291779398262526 0.319177879181666 chr12 133851895 7626529 0.05697737039882775 0.29695287782680446 chr13 115169878 3562532 0.030932845131606372 0.20617628246758843 chr14 107349540 4424949 0.041220008953927516 0.33181608983358013 chr15 102531392 4184887 0.04081566550856932 0.2328641272293819 chr16 90354753 3883903 0.0429850436312963 0.320704786862181 chr17 81195210 3568124 0.043945006115508535 0.25008649218647544 chr18 78077248 3841392 0.04919988983218261 0.7934836408623555 chr19 59128983 3236974 0.05474428674005775 0.4549344333662549 chr20 63025520 2486556 0.03945316119565535 0.2443183741247408 chr21 48129895 2871891 0.059669587893345706 0.3319142757933779 chr22 51304566 1379060 0.02687986874306665 0.18579356109342499 chrMT 16571 354830 21.41270894936938 11.369314991964057 chrX 155270560 4600022 0.029625847939235873 0.23208472919251333 chrY 59373566 384635 0.0064782196171272585 0.1646450443016063