BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237609.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 = 1,196,337 number of mapped reads = 1,033,735 (86.41%) number of supplementary alignments = 5,687 (0.48%) number of secondary alignments = 0 number of mapped bases = 65,940,132 bp number of sequenced bases = 65,904,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,869 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1713 >>>>>>> ACTG content number of A's = 17,714,881 bp (26.88%) number of C's = 11,106,793 bp (16.85%) number of T's = 22,007,013 bp (33.39%) number of G's = 14,955,417 bp (22.69%) number of N's = 120,601 bp (0.18%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 577,208 number of insertions = 5,405 mapped reads with insertion percentage = 0.52% number of deletions = 21,851 mapped reads with deletion percentage = 2.08% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2005X There is a 1.81% of reference with a coverageData >= 1X There is a 0.25% 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% 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 5268124 0.021135851051701092 0.20260320765862647 chr2 243199373 6638478 0.027296443728907147 0.29137016920780046 chr3 198022430 4391361 0.022176078740171 0.17146784280098962 chr4 191154276 3788262 0.01981782505351855 0.1711470473383107 chr5 180915260 2252538 0.012450790497164252 0.12711364226171173 chr6 171115067 4573942 0.02673021189887387 0.21438149558614703 chr7 159138663 3089197 0.019411982869304362 0.20964400684751966 chr8 146364022 4318147 0.02950278996842544 0.3071730492665493 chr9 141213431 3466189 0.024545745935455672 0.20943247227663064 chr10 135534747 3178799 0.02345375684362328 0.20600402504562393 chr11 135006516 4063134 0.03009583626319192 0.21852485809149608 chr12 133851895 3608373 0.02695795229496004 0.1915089426178973 chr13 115169878 1547489 0.013436577574563376 0.13625724891344604 chr14 107349540 2482094 0.02312160815966235 0.17762020345643392 chr15 102531392 1566145 0.015274785306728305 0.14333245569623426 chr16 90354753 1094727 0.012115876184178158 0.1325320224613949 chr17 81195210 1680930 0.020702329607867262 0.17211630117405288 chr18 78077248 1318026 0.016881050930483615 0.23898107447570693 chr19 59128983 693254 0.011724436390187871 0.14727040289176957 chr20 63025520 1503967 0.0238628257251983 0.1783568568916898 chr21 48129895 576503 0.011978064776580128 0.13326973208985082 chr22 51304566 328717 0.00640716851595626 0.08853426925722907 chrMT 16571 7673 0.46303783718544445 0.8124393081772823 chrX 155270560 4321680 0.02783322221546699 0.19805553436440976 chrY 59373566 182383 0.003071787872737844 0.08411000649936665