BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472689.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 = 14,315,992 number of mapped reads = 14,191,937 (99.13%) number of supplementary alignments = 92,860 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,130,054 number of mapped paired reads (second in pair) = 7,061,883 number of mapped paired reads (both in pair) = 14,118,908 number of mapped paired reads (singletons) = 73,029 number of mapped bases = 1,395,867,003 bp number of sequenced bases = 1,395,013,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,490,547 duplication rate = 46.77% >>>>>>> Insert size mean insert size = 17,869.1699 std insert size = 1,289,170.035 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.8048 >>>>>>> ACTG content number of A's = 371,062,810 bp (26.6%) number of C's = 326,470,931 bp (23.4%) number of T's = 375,639,085 bp (26.93%) number of G's = 321,543,749 bp (23.05%) number of N's = 297,322 bp (0.02%) GC percentage = 46.45% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 6,834,903 number of insertions = 100,914 mapped reads with insertion percentage = 0.7% number of deletions = 119,274 mapped reads with deletion percentage = 0.83% homopolymer indels = 40.82% >>>>>>> Coverage mean coverageData = 0.4509X std coverageData = 53.3535X There is a 2.64% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 135661727 0.5442783911860344 25.02688531445999 chr2 243199373 110313040 0.45359097204580373 78.64124724310166 chr3 198022430 81463058 0.4113829832307381 17.243578853486298 chr4 191154276 37007107 0.19359811234356064 13.378009753259688 chr5 180915260 79581426 0.4398823294397609 23.42202043132721 chr6 171115067 90815382 0.5307269756671983 21.40461107484957 chr7 159138663 119710755 0.7522418043690615 37.3159721325612 chr8 146364022 56003036 0.38262843036658284 22.038206550130848 chr9 141213431 46329651 0.3280824683028911 19.32471982863922 chr10 135534747 29624003 0.2185712789946035 15.386457002282281 chr11 135006516 40110970 0.2971039560786829 14.585372955357089 chr12 133851895 43754911 0.32689048593596676 15.762967136595206 chr13 115169878 41961346 0.3643430619940398 40.579082930717256 chr14 107349540 33131291 0.3086300230070851 16.522244284740506 chr15 102531392 18942443 0.18474774047737497 10.1124148321567 chr16 90354753 79236875 0.8769530364384927 46.65205104596383 chr17 81195210 175170449 2.1573988046831825 262.8479736193909 chr18 78077248 10533904 0.13491643557928681 4.942481551370311 chr19 59128983 61295188 1.0366352487408754 65.21352395493237 chr20 63025520 27093950 0.4298885594279904 28.20716793023056 chr21 48129895 10838512 0.22519292842837077 18.616772239661746 chr22 51304566 26044046 0.5076360260020522 23.557403770396515 chrMT 16571 600 0.03620783296119727 0.18680692116046266 chrX 155270560 40379289 0.260057598813323 19.152925328597398 chrY 59373566 864044 0.014552671469993903 0.5665557803249253