BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231868.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 = 4,466,314 number of mapped reads = 3,997,358 (89.5%) number of supplementary alignments = 25,375 (0.57%) number of secondary alignments = 0 number of mapped bases = 254,539,040 bp number of sequenced bases = 254,444,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 352,124 duplication rate = 6.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7178 >>>>>>> ACTG content number of A's = 66,846,356 bp (26.27%) number of C's = 45,907,949 bp (18.04%) number of T's = 81,774,734 bp (32.14%) number of G's = 59,819,625 bp (23.51%) number of N's = 95,487 bp (0.04%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,684,305 number of insertions = 18,050 mapped reads with insertion percentage = 0.45% number of deletions = 55,576 mapped reads with deletion percentage = 1.38% homopolymer indels = 44% >>>>>>> Coverage mean coverageData = 0.0822X std coverageData = 0.919X There is a 6.52% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 28265598 0.1134023172604252 1.9169757299966188 chr2 243199373 15366603 0.06318520812962787 1.3695416125010451 chr3 198022430 22870119 0.11549256819038126 0.4212274535311659 chr4 191154276 10241525 0.05357727388740182 0.38219789140102456 chr5 180915260 15402764 0.08513800328396842 0.37042444547220554 chr6 171115067 16888980 0.09869954935061329 0.6364812650829688 chr7 159138663 14714878 0.09246576364663815 1.1660640547147512 chr8 146364022 13863346 0.09471826348144491 1.2023078382730272 chr9 141213431 11945977 0.08459518981590355 0.7135203166210076 chr10 135534747 7468619 0.055104828579493344 0.4952521019639507 chr11 135006516 10692097 0.07919689594834074 0.7018810791384452 chr12 133851895 7289911 0.05446251620120881 0.31968871862232867 chr13 115169878 13597180 0.11806194671839454 0.4503524056651703 chr14 107349540 12363767 0.11517298537096665 0.504127222902862 chr15 102531392 5635427 0.054962942471316494 0.4075760029002603 chr16 90354753 7931291 0.08777945527669143 0.47125916027440656 chr17 81195210 6383097 0.07861420642917236 0.42825375645939867 chr18 78077248 5196726 0.06655877522732359 1.724758450086866 chr19 59128983 6691073 0.11316063054898137 1.1518567743791785 chr20 63025520 5901218 0.09363219851260252 0.4452379754125194 chr21 48129895 4210437 0.08748070196288606 0.3977353324126295 chr22 51304566 1974262 0.03848121432310723 0.2330079722793499 chrMT 16571 97921 5.909178685655664 4.348427232977419 chrX 155270560 8954059 0.05766746123669548 0.4441111731734583 chrY 59373566 592165 0.009973546140044882 0.1955979350874661