BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818773.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,048,732 number of mapped reads = 1,926,402 (94.03%) number of supplementary alignments = 15,040 (0.73%) number of secondary alignments = 0 number of mapped bases = 130,878,248 bp number of sequenced bases = 130,823,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 934,605 duplication rate = 41.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7465 >>>>>>> ACTG content number of A's = 37,903,248 bp (28.97%) number of C's = 27,725,662 bp (21.19%) number of T's = 38,181,264 bp (29.19%) number of G's = 27,004,656 bp (20.64%) number of N's = 8,361 bp (0.01%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 683,961 number of insertions = 15,466 mapped reads with insertion percentage = 0.79% number of deletions = 34,060 mapped reads with deletion percentage = 1.75% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.5353X There is a 1.83% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% 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 10656695 0.042754938612570195 0.6974812999381954 chr2 243199373 11629125 0.04781724910121376 0.9109985299844283 chr3 198022430 8988013 0.04538886327170109 0.4100620739275097 chr4 191154276 8660695 0.045307356870217225 0.4692654002198809 chr5 180915260 8166996 0.0451426596075975 0.4232388984063364 chr6 171115067 7811006 0.04564768104260509 0.4521298267692954 chr7 159138663 7195757 0.045216899930848355 0.46921630842477047 chr8 146364022 6783236 0.04634496857431261 0.4671803009471487 chr9 141213431 5548228 0.0392896621851784 0.44123134320823243 chr10 135534747 6314957 0.04659290063824002 0.5718406332584943 chr11 135006516 6115339 0.045296621090496106 0.4531457150703073 chr12 133851895 6098160 0.045559011323672335 0.44477180965306495 chr13 115169878 4279996 0.03716246013562678 0.3697281304616268 chr14 107349540 3994851 0.037213489689848694 0.4192424256807861 chr15 102531392 3737665 0.0364538599066323 0.36944467069647674 chr16 90354753 3814839 0.04222067875056888 0.5777343417799606 chr17 81195210 3451990 0.042514700066666494 0.4170781537251524 chr18 78077248 3567714 0.04569466895144665 0.577025814170024 chr19 59128983 2516537 0.0425601265626368 0.61501922136293 chr20 63025520 2828832 0.044883913690835074 0.43560401428039686 chr21 48129895 1732271 0.035991580700518874 0.38292269705906923 chr22 51304566 1544882 0.030111978727195548 0.37237129668607494 chrMT 16571 166437 10.043871824271317 10.656010422769173 chrX 155270560 4079321 0.026272340358661682 0.33531004496494526 chrY 59373566 1194706 0.020121850184979626 0.8193707017168718