BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063607.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,150,237 number of mapped reads = 3,895,729 (93.87%) number of supplementary alignments = 27,981 (0.67%) number of secondary alignments = 0 number of mapped bases = 251,760,988 bp number of sequenced bases = 251,656,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 366,216 duplication rate = 7.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3117 >>>>>>> ACTG content number of A's = 66,522,836 bp (26.43%) number of C's = 45,031,137 bp (17.89%) number of T's = 82,173,538 bp (32.65%) number of G's = 57,900,193 bp (23.01%) number of N's = 28,671 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,405,673 number of insertions = 16,417 mapped reads with insertion percentage = 0.42% number of deletions = 60,297 mapped reads with deletion percentage = 1.53% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0813X std coverageData = 0.9381X There is a 6.46% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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% 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 25105433 0.10072365276072873 1.8897497502335534 chr2 243199373 24849862 0.10217897231174194 1.2673591745162012 chr3 198022430 18070770 0.09125617739364172 0.3709438420927162 chr4 191154276 12146961 0.06354532712624227 0.3340218240542282 chr5 180915260 11538017 0.063775808629963 0.32024447558654173 chr6 171115067 16659513 0.09735853944410401 0.51774123670947 chr7 159138663 18775755 0.11798361658976612 1.8715211081736614 chr8 146364022 10864304 0.07422796840059506 0.994381906877094 chr9 141213431 8840549 0.06260416546355282 0.7913830976748697 chr10 135534747 12094362 0.08923440127128433 0.6560606958436367 chr11 135006516 10410981 0.07711465571039548 0.5846745028344268 chr12 133851895 11485867 0.08581026813255054 0.4141176524966558 chr13 115169878 7297948 0.06336681193671144 0.33826332425559585 chr14 107349540 5755353 0.05361320598113415 0.41283963781985406 chr15 102531392 6418396 0.06259932567773975 0.35038045153594605 chr16 90354753 5910808 0.06541778715282416 0.3962628314509673 chr17 81195210 6930623 0.08535753525361903 0.4303843097948167 chr18 78077248 7452713 0.09545306975983579 1.5397577424597457 chr19 59128983 5359377 0.09063874817532376 1.2227361878902174 chr20 63025520 4646692 0.07372715052569181 0.3724995475236868 chr21 48129895 4121937 0.08564192795350997 0.38495969776146405 chr22 51304566 2277633 0.0443943527365576 0.24746166513928075 chrMT 16571 114630 6.917506487236738 4.7358532372857685 chrX 155270560 13945627 0.08981501064979736 0.49096383161645396 chrY 59373566 686877 0.01156873414003801 0.3431188923994968