BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093998.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 345,044 number of mapped reads = 332,251 (96.29%) number of supplementary alignments = 23,296 (6.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 167,170 number of mapped paired reads (second in pair) = 165,081 number of mapped paired reads (both in pair) = 329,020 number of mapped paired reads (singletons) = 3,231 number of mapped bases = 42,819,394 bp number of sequenced bases = 42,099,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 315,310 duplication rate = 51.66% >>>>>>> Insert size mean insert size = 1,288,154.6401 std insert size = 10,319,230.718 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 40.2065 >>>>>>> ACTG content number of A's = 10,985,545 bp (26.09%) number of C's = 9,980,421 bp (23.71%) number of T's = 10,415,409 bp (24.74%) number of G's = 10,717,681 bp (25.46%) number of N's = 469 bp (0%) GC percentage = 49.16% >>>>>>> Mismatches and indels general error rate = 0.0337 number of mismatches = 1,367,986 number of insertions = 22,628 mapped reads with insertion percentage = 6.68% number of deletions = 110,977 mapped reads with deletion percentage = 32.09% homopolymer indels = 30.6% >>>>>>> Coverage mean coverageData = 0.0138X std coverageData = 2.7937X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 611969 0.002455235608018806 0.7724231789543082 chr2 243199373 1942816 0.007988573227119298 2.5638928373760645 chr3 198022430 788045 0.003979574435077885 1.412365929904642 chr4 191154276 1041311 0.005447489963551744 1.7849708627962213 chr5 180915260 413248 0.0022842075345109085 1.0952266065782583 chr6 171115067 885445 0.005174558941674025 1.5769466106396994 chr7 159138663 786113 0.004939798947537972 1.3833600489524258 chr8 146364022 535074 0.0036557754609940958 1.2721388857514697 chr9 141213431 581040 0.004114622779755277 1.298201204334216 chr10 135534747 682368 0.005034635140463279 1.4507612741101936 chr11 135006516 892362 0.006609769857330442 1.8356050123318617 chr12 133851895 936986 0.007000169851909829 1.6546750354543496 chr13 115169878 935644 0.00812403395964351 2.344771211169481 chr14 107349540 132156 0.0012310811951313438 0.4199848977124784 chr15 102531392 637037 0.006213092279094387 1.665964244727721 chr16 90354753 243545 0.002695430975280293 0.6934214959422024 chr17 81195210 1127985 0.013892260393193145 3.5337857964973143 chr18 78077248 215135 0.0027554121784620278 0.7342969915003812 chr19 59128983 133949 0.0022653695904088188 0.5970754705697194 chr20 63025520 421004 0.006679897286051745 2.4482207647315937 chr21 48129895 101622 0.00211141121334256 0.38027491106704553 chr22 51304566 140152 0.002731764654241496 0.8466220893138994 chrMT 16571 1358432 81.97646490857522 340.7926487717707 chrX 155270560 26564944 0.1710880929391895 9.548203766407873 chrY 59373566 711012 0.011975228168036934 1.868309742312267