BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081985.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,493,990 number of mapped reads = 2,338,470 (93.76%) number of supplementary alignments = 16,499 (0.66%) number of secondary alignments = 0 number of mapped bases = 161,825,024 bp number of sequenced bases = 161,766,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,201 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1576 >>>>>>> ACTG content number of A's = 46,763,435 bp (28.91%) number of C's = 30,068,225 bp (18.59%) number of T's = 51,055,977 bp (31.56%) number of G's = 33,857,483 bp (20.93%) number of N's = 21,160 bp (0.01%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,177,049 number of insertions = 11,274 mapped reads with insertion percentage = 0.48% number of deletions = 32,955 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.3748X There is a 4.41% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 14637694 0.05872681055426538 0.565495702939692 chr2 243199373 14162559 0.05823435654992416 0.4655642384033315 chr3 198022430 10508323 0.053066326880242806 0.26343826667125225 chr4 191154276 8424653 0.04407253228277248 0.2507636280053049 chr5 180915260 8163173 0.04512152816738621 0.2424613826940915 chr6 171115067 14725551 0.08605642541109486 0.40441740137351057 chr7 159138663 10425514 0.06551213767580792 0.4525115589508806 chr8 146364022 9198717 0.06284821142725909 0.5971090991087527 chr9 141213431 7857153 0.055640266965824234 0.38909030986381327 chr10 135534747 6759400 0.049872081880228104 0.38526959370728114 chr11 135006516 7270677 0.05385426730069828 0.31498334032657865 chr12 133851895 6749380 0.05042423941775348 0.26242729256160646 chr13 115169878 4329902 0.037595785245166276 0.22085600118172966 chr14 107349540 4101485 0.03820682417456097 0.23758931231553984 chr15 102531392 3528443 0.034413294613224406 0.21196403223870125 chr16 90354753 3406392 0.03770019713296101 0.2471906963956368 chr17 81195210 4252847 0.052378052843265015 0.2760584707628148 chr18 78077248 4641372 0.05944589645372747 0.5724931700216946 chr19 59128983 3120778 0.05277915908007415 0.4381401892882973 chr20 63025520 4189338 0.06647050274238119 0.2993055139394639 chr21 48129895 1763392 0.03663818506148829 0.23763602653799276 chr22 51304566 1240458 0.024178315824755246 0.1736658557173084 chrMT 16571 44752 2.700621567799167 2.3183092380187236 chrX 155270560 7992531 0.0514748642627424 0.28426386565991507 chrY 59373566 330540 0.00556712392851728 0.13150389165640147