BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472378.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,203,194 number of mapped reads = 19,038,462 (99.14%) number of supplementary alignments = 71,084 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,556,396 number of mapped paired reads (second in pair) = 9,482,066 number of mapped paired reads (both in pair) = 18,927,200 number of mapped paired reads (singletons) = 111,262 number of mapped bases = 1,867,290,746 bp number of sequenced bases = 1,867,078,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,889,296 duplication rate = 47.75% >>>>>>> Insert size mean insert size = 17,269.5089 std insert size = 1,274,467.8578 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 54.847 >>>>>>> ACTG content number of A's = 506,589,205 bp (27.13%) number of C's = 428,210,233 bp (22.93%) number of T's = 507,560,556 bp (27.18%) number of G's = 424,488,561 bp (22.74%) number of N's = 230,444 bp (0.01%) GC percentage = 45.67% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 9,958,885 number of insertions = 109,692 mapped reads with insertion percentage = 0.57% number of deletions = 90,349 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.6032X std coverageData = 17.5208X There is a 5.38% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 162999820 0.6539595341670181 17.92423535603895 chr2 243199373 142311524 0.5851640250733705 16.9434817668475 chr3 198022430 133541865 0.6743774682494301 13.857222388623125 chr4 191154276 41890475 0.219144849263011 7.286123818684829 chr5 180915260 78200284 0.4322481365032447 14.1097796235151 chr6 171115067 156413408 0.914083199932359 21.620494987679184 chr7 159138663 171073223 1.0749947233124613 29.41261852529552 chr8 146364022 80276863 0.5484740163808836 16.310191481488086 chr9 141213431 57272676 0.4055752742102839 9.032626071801275 chr10 135534747 56018659 0.4133158488132936 11.41912518387354 chr11 135006516 54682678 0.40503732427255584 12.59953645580052 chr12 133851895 101295209 0.756770824947977 16.93536062053736 chr13 115169878 71751976 0.6230099158392788 20.72760394969784 chr14 107349540 33038623 0.3077667868907496 8.720411818608452 chr15 102531392 25604086 0.24971948103464742 7.189880439818484 chr16 90354753 99738320 1.1038525001556918 29.305509332092953 chr17 81195210 87541428 1.0781600047589015 23.308094484974024 chr18 78077248 26177488 0.3352767761486675 11.890709208443248 chr19 59128983 51577417 0.8722865570003123 20.04437262359945 chr20 63025520 80405251 1.275757042544036 35.43614334300395 chr21 48129895 15059678 0.3128965479770941 18.201541619370275 chr22 51304566 13398599 0.2611580224652909 6.590561276780092 chrMT 16571 3172 0.19141874358819624 0.5172085280398744 chrX 155270560 126577743 0.8152076156613334 18.574917720235057 chrY 59373566 440281 0.007415438041905719 0.6550209878675273