BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975305.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 56,487,804 number of mapped reads = 56,288,911 (99.65%) number of supplementary alignments = 111,533 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,136,089 number of mapped paired reads (second in pair) = 28,152,822 number of mapped paired reads (both in pair) = 56,201,748 number of mapped paired reads (singletons) = 87,163 number of mapped bases = 5,120,234,601 bp number of sequenced bases = 5,118,598,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,061,021 duplication rate = 43.43% >>>>>>> Insert size mean insert size = 62,963.7825 std insert size = 2,467,909.6572 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 55.7529 >>>>>>> ACTG content number of A's = 1,330,207,811 bp (25.99%) number of C's = 1,129,611,815 bp (22.07%) number of T's = 1,402,024,235 bp (27.39%) number of G's = 1,256,660,576 bp (24.55%) number of N's = 93,970 bp (0%) GC percentage = 46.62% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 29,421,272 number of insertions = 459,316 mapped reads with insertion percentage = 0.81% number of deletions = 1,107,081 mapped reads with deletion percentage = 1.94% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 1.654X std coverageData = 24.5585X There is a 14.71% of reference with a coverageData >= 1X There is a 8.01% of reference with a coverageData >= 2X There is a 4.61% of reference with a coverageData >= 3X There is a 3.38% of reference with a coverageData >= 4X There is a 2.57% of reference with a coverageData >= 5X There is a 2.19% of reference with a coverageData >= 6X There is a 1.92% of reference with a coverageData >= 7X There is a 1.76% of reference with a coverageData >= 8X There is a 1.63% of reference with a coverageData >= 9X There is a 1.54% of reference with a coverageData >= 10X There is a 1.46% of reference with a coverageData >= 11X There is a 1.4% of reference with a coverageData >= 12X There is a 1.35% of reference with a coverageData >= 13X There is a 1.3% of reference with a coverageData >= 14X There is a 1.26% of reference with a coverageData >= 15X There is a 1.22% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.15% of reference with a coverageData >= 18X There is a 1.12% of reference with a coverageData >= 19X There is a 1.09% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 1.04% of reference with a coverageData >= 22X There is a 1.01% of reference with a coverageData >= 23X There is a 0.99% of reference with a coverageData >= 24X There is a 0.97% of reference with a coverageData >= 25X There is a 0.95% of reference with a coverageData >= 26X There is a 0.93% of reference with a coverageData >= 27X There is a 0.91% of reference with a coverageData >= 28X There is a 0.89% of reference with a coverageData >= 29X There is a 0.87% of reference with a coverageData >= 30X There is a 0.85% of reference with a coverageData >= 31X There is a 0.84% of reference with a coverageData >= 32X There is a 0.82% of reference with a coverageData >= 33X There is a 0.81% of reference with a coverageData >= 34X There is a 0.79% of reference with a coverageData >= 35X There is a 0.78% of reference with a coverageData >= 36X There is a 0.77% of reference with a coverageData >= 37X There is a 0.75% of reference with a coverageData >= 38X There is a 0.74% of reference with a coverageData >= 39X There is a 0.73% of reference with a coverageData >= 40X There is a 0.72% of reference with a coverageData >= 41X There is a 0.71% of reference with a coverageData >= 42X There is a 0.69% of reference with a coverageData >= 43X There is a 0.68% of reference with a coverageData >= 44X There is a 0.67% of reference with a coverageData >= 45X There is a 0.66% of reference with a coverageData >= 46X There is a 0.65% of reference with a coverageData >= 47X There is a 0.64% of reference with a coverageData >= 48X There is a 0.63% of reference with a coverageData >= 49X There is a 0.62% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 630712667 2.5304356894661457 34.03855487787774 chr2 243199373 361156087 1.4850206336675054 20.63175679974154 chr3 198022430 315104574 1.5912569803329855 22.954434715707507 chr4 191154276 222691333 1.1649822209574847 19.755283800841546 chr5 180915260 249376273 1.3784148059152113 19.668071712301234 chr6 171115067 401490664 2.346319766219067 37.281870028116174 chr7 159138663 273998111 1.7217570251925518 28.098411827501952 chr8 146364022 178148063 1.2171574719366485 17.47883890458671 chr9 141213431 216062378 1.530041274898278 21.765172287809776 chr10 135534747 204059898 1.5055910201389169 22.339665339427864 chr11 135006516 249133631 1.8453452350403592 24.013015876887813 chr12 133851895 255546796 1.909175779692921 24.400386036316224 chr13 115169878 102256402 0.887874536083124 16.169674110761548 chr14 107349540 168935945 1.57369975688764 22.179331715537145 chr15 102531392 186777138 1.8216580732659906 26.19946416430948 chr16 90354753 174364368 1.9297752714790777 25.295833633984323 chr17 81195210 203845048 2.510555093089851 29.386827618685246 chr18 78077248 92998461 1.1911083367077693 19.89400676735159 chr19 59128983 219522301 3.7126006547415167 39.49005231660609 chr20 63025520 130974575 2.07811970452604 26.878067970091397 chr21 48129895 52512054 1.0910485884085142 19.90753382165506 chr22 51304566 89144378 1.7375525211537701 22.075058964502148 chrMT 16571 56613 3.4163900790537687 4.282527988568183 chrX 155270560 130315461 0.8392799059911937 13.793572087571103 chrY 59373566 11051382 0.18613303435404233 4.136108692125369