BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084970.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 = 2,639,858 number of mapped reads = 2,395,471 (90.74%) number of supplementary alignments = 25,529 (0.97%) number of secondary alignments = 0 number of mapped bases = 162,861,044 bp number of sequenced bases = 162,797,597 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,620 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1663 >>>>>>> ACTG content number of A's = 47,403,041 bp (29.12%) number of C's = 30,179,296 bp (18.54%) number of T's = 50,564,781 bp (31.06%) number of G's = 34,627,872 bp (21.27%) number of N's = 22,607 bp (0.01%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,392,770 number of insertions = 13,856 mapped reads with insertion percentage = 0.57% number of deletions = 38,764 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.0526X std coverageData = 0.5654X There is a 4.73% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.04% 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% 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 12957815 0.051987092140484574 1.2159341105576356 chr2 243199373 13741292 0.05650216869596946 0.5686222637587446 chr3 198022430 11259608 0.05686026577898271 0.2650466728479945 chr4 191154276 11418422 0.05973406527406167 0.2748132061068113 chr5 180915260 10620441 0.058703953442070064 0.2636360817045736 chr6 171115067 9697993 0.056675272201482996 0.39171271337147023 chr7 159138663 9035696 0.056778760294096474 0.4828112377070109 chr8 146364022 8688390 0.05936151440276764 0.923226949227665 chr9 141213431 6840108 0.04843808376839169 0.4798854433199741 chr10 135534747 7646535 0.056417525167918744 0.6307322881132343 chr11 135006516 7504060 0.05558294682606282 0.49696918428639514 chr12 133851895 7337306 0.054816601587896835 0.2623045547027406 chr13 115169878 5213883 0.04527123837015786 0.22520393660715 chr14 107349540 4697667 0.04376047629081596 0.26502086944258707 chr15 102531392 4260317 0.041551342636604406 0.22105403492453451 chr16 90354753 4171031 0.046162828866346414 0.321714410230125 chr17 81195210 3864920 0.04760034489719283 0.30776068887331426 chr18 78077248 4540247 0.058150704799431456 1.0031282798137506 chr19 59128983 2572491 0.04350643067884323 0.8404591970980053 chr20 63025520 3073243 0.04876188248823651 0.2609496369074478 chr21 48129895 2128484 0.04422374077483444 0.25499436717971286 chr22 51304566 1507508 0.029383505553872143 0.18186437275212922 chrMT 16571 40858 2.465632731880997 2.1973256526404232 chrX 155270560 9654733 0.06218006169360116 0.33980234680832994 chrY 59373566 387996 0.006534827300081656 0.14364271479170876