BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714238.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 295,152 number of mapped reads = 26,859 (9.1%) number of supplementary alignments = 963 (0.33%) number of secondary alignments = 0 number of mapped bases = 2,833,285 bp number of sequenced bases = 2,783,146 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,420 duplication rate = 38.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.0703 >>>>>>> ACTG content number of A's = 608,315 bp (21.86%) number of C's = 428,945 bp (15.41%) number of T's = 547,474 bp (19.67%) number of G's = 1,198,351 bp (43.06%) number of N's = 61 bp (0%) GC percentage = 58.47% >>>>>>> Mismatches and indels general error rate = 0.0396 number of mismatches = 99,223 number of insertions = 2,857 mapped reads with insertion percentage = 9.11% number of deletions = 7,926 mapped reads with deletion percentage = 27.73% homopolymer indels = 31.59% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 0.8923X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 107032 4.294151788693036E-4 0.1266240045666176 chr2 243199373 920418 0.0037846232440739065 3.1282568959011177 chr3 198022430 123511 6.237222722698636E-4 0.18994052974866305 chr4 191154276 66089 3.457364458852074E-4 0.08824799207297665 chr5 180915260 146877 8.118552299015572E-4 0.1904244405980297 chr6 171115067 126116 7.370245192961295E-4 0.17507704846591488 chr7 159138663 82288 5.170836454746387E-4 0.16199589159713632 chr8 146364022 140982 9.632285180028737E-4 0.2690990787961762 chr9 141213431 41553 2.942567127343574E-4 0.09109527515788837 chr10 135534747 52371 3.8640275766331717E-4 0.09788303266837112 chr11 135006516 71566 5.300929326996336E-4 0.1491267428454165 chr12 133851895 78828 5.889195666598519E-4 0.14187988502918267 chr13 115169878 38116 3.3095459213736426E-4 0.08458313714197319 chr14 107349540 77896 7.256295648775021E-4 0.17006037648889705 chr15 102531392 53436 5.211672148174873E-4 0.1329371497223239 chr16 90354753 16677 1.8457247069227228E-4 0.04714441154390816 chr17 81195210 28905 3.5599390653709743E-4 0.09936901327880648 chr18 78077248 34605 4.4321490429580717E-4 0.1177069419889604 chr19 59128983 18994 3.212299457272925E-4 0.09426664567299954 chr20 63025520 33074 5.247715528566841E-4 0.12365191231698573 chr21 48129895 22043 4.57989779533074E-4 0.11330181981960921 chr22 51304566 12417 2.4202524196384391E-4 0.09527692410706803 chrMT 16571 3340 0.20155693681733147 1.482340778205208 chrX 155270560 532617 0.0034302510405063266 0.41846523486163595 chrY 59373566 3534 5.952143753669773E-5 0.01232405106906184