BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238602.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,361,462 number of mapped reads = 1,660,810 (70.33%) number of supplementary alignments = 13,870 (0.59%) number of secondary alignments = 0 number of mapped bases = 100,518,763 bp number of sequenced bases = 100,464,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,073,663 duplication rate = 28.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7675 >>>>>>> ACTG content number of A's = 24,367,381 bp (24.25%) number of C's = 16,443,411 bp (16.37%) number of T's = 36,407,112 bp (36.24%) number of G's = 23,244,639 bp (23.14%) number of N's = 2,178 bp (0%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 638,061 number of insertions = 7,450 mapped reads with insertion percentage = 0.45% number of deletions = 33,054 mapped reads with deletion percentage = 1.97% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 2.7739X There is a 0.39% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6434495 0.02581536196052246 1.4115197934401265 chr2 243199373 12267688 0.05044292610080043 3.0675066127791917 chr3 198022430 6948887 0.03509141363430395 1.7301691144880902 chr4 191154276 7196746 0.03764888837746951 1.7339103976504635 chr5 180915260 4681124 0.025874677459491256 1.3799205561048846 chr6 171115067 5335698 0.03118192975958102 2.114282713229908 chr7 159138663 5947328 0.03737198671827474 2.0144376390198375 chr8 146364022 3776384 0.025801313385607837 1.9167263312226648 chr9 141213431 3583844 0.02537891739207158 1.4711398439068513 chr10 135534747 4751409 0.03505675928254767 1.6427643359986073 chr11 135006516 5946429 0.044045496292934486 1.8652876414594362 chr12 133851895 4468456 0.033383584147239756 1.683932342215492 chr13 115169878 2902211 0.025199392848189003 2.261305066745241 chr14 107349540 2357557 0.021961500719984456 1.7391791009887294 chr15 102531392 2411375 0.02351840692848489 1.7650276732888794 chr16 90354753 1741519 0.01927423784778649 1.1854035682591426 chr17 81195210 2038111 0.025101369896081308 1.3059957927118941 chr18 78077248 4949618 0.06339385834910574 13.145694237156285 chr19 59128983 1753259 0.029651431684526015 1.5416804666850967 chr20 63025520 2044032 0.032431814921955425 1.5482225226884203 chr21 48129895 1231242 0.025581647331663616 1.3923110055366141 chr22 51304566 1189515 0.023185363267667052 1.7150314221522542 chrMT 16571 11297 0.681733148271076 3.878003713886426 chrX 155270560 6222748 0.04007680528749301 1.7614865665408035 chrY 59373566 327791 0.005520823862929169 0.8646295354865791