BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082953.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 = 1,583,464 number of mapped reads = 1,458,122 (92.08%) number of supplementary alignments = 15,723 (0.99%) number of secondary alignments = 0 number of mapped bases = 98,407,686 bp number of sequenced bases = 98,370,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,442 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0994 >>>>>>> ACTG content number of A's = 27,605,767 bp (28.06%) number of C's = 17,842,326 bp (18.14%) number of T's = 31,747,100 bp (32.27%) number of G's = 21,170,478 bp (21.52%) number of N's = 4,561 bp (0%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 713,130 number of insertions = 8,242 mapped reads with insertion percentage = 0.56% number of deletions = 23,005 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.0318X std coverageData = 0.2797X There is a 2.7% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% 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 10272249 0.04121253122173766 0.40004550153200663 chr2 243199373 10422780 0.04285693614843324 0.4028345409099315 chr3 198022430 7222808 0.03647469632606771 0.2174057503917261 chr4 191154276 5607685 0.029335911899768332 0.19934145955992733 chr5 180915260 5058323 0.027959625959689635 0.19054281863951222 chr6 171115067 7237202 0.042294358567501245 0.2709626098626982 chr7 159138663 5824872 0.03660249426627393 0.3097667289247428 chr8 146364022 7801256 0.05330036639741972 0.4111411530362519 chr9 141213431 3254727 0.023048282142510933 0.2775540038136333 chr10 135534747 3105309 0.022911534265084067 0.20292143713966967 chr11 135006516 3309519 0.024513772357476434 0.20709709504546275 chr12 133851895 2673321 0.01997223124857515 0.16768350827961132 chr13 115169878 2229053 0.01935447912864855 0.15869530531081522 chr14 107349540 2208699 0.02057483432160026 0.17975390057102064 chr15 102531392 1712448 0.01670169463806753 0.1531036296899597 chr16 90354753 3684998 0.04078366524891059 0.2450689922674452 chr17 81195210 2522915 0.03107221472793777 0.206926820698254 chr18 78077248 3831089 0.04906793077542897 0.5607459009700286 chr19 59128983 865052 0.014629915079040002 0.2740090923536626 chr20 63025520 1816053 0.02881456590917457 0.19700730220120646 chr21 48129895 2299051 0.047767629661357044 0.25833286893080426 chr22 51304566 1278010 0.024910258474849976 0.17861273047688356 chrMT 16571 4341 0.26196367147426225 0.5702062944941464 chrX 155270560 3984764 0.025663358205187125 0.1966514810034473 chrY 59373566 181162 0.0030512231655413793 0.07347067318808302