BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365348.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 378,934,234 number of mapped reads = 349,266,910 (92.17%) number of supplementary alignments = 1,662,254 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 174,972,350 number of mapped paired reads (second in pair) = 174,294,560 number of mapped paired reads (both in pair) = 347,293,126 number of mapped paired reads (singletons) = 1,973,784 number of mapped bases = 35,518,170,912 bp number of sequenced bases = 35,505,783,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 250,360,954 duplication rate = 42.57% >>>>>>> Insert size mean insert size = 76,118.5541 std insert size = 2,659,798.3182 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.6674 >>>>>>> ACTG content number of A's = 10,675,451,041 bp (30.07%) number of C's = 6,918,441,719 bp (19.49%) number of T's = 10,315,839,291 bp (29.05%) number of G's = 7,594,190,995 bp (21.39%) number of N's = 1,860,328 bp (0.01%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 207,212,673 number of insertions = 10,776,188 mapped reads with insertion percentage = 3.01% number of deletions = 5,787,786 mapped reads with deletion percentage = 1.61% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 11.4734X std coverageData = 136.5197X There is a 75% of reference with a coverageData >= 1X There is a 68.51% of reference with a coverageData >= 2X There is a 62.58% of reference with a coverageData >= 3X There is a 58.29% of reference with a coverageData >= 4X There is a 53.95% of reference with a coverageData >= 5X There is a 50.53% of reference with a coverageData >= 6X There is a 46.96% of reference with a coverageData >= 7X There is a 44.04% of reference with a coverageData >= 8X There is a 40.98% of reference with a coverageData >= 9X There is a 38.42% of reference with a coverageData >= 10X There is a 35.76% of reference with a coverageData >= 11X There is a 33.5% of reference with a coverageData >= 12X There is a 31.18% of reference with a coverageData >= 13X There is a 29.18% of reference with a coverageData >= 14X There is a 27.15% of reference with a coverageData >= 15X There is a 25.38% of reference with a coverageData >= 16X There is a 23.6% of reference with a coverageData >= 17X There is a 22.04% of reference with a coverageData >= 18X There is a 20.49% of reference with a coverageData >= 19X There is a 19.13% of reference with a coverageData >= 20X There is a 17.78% of reference with a coverageData >= 21X There is a 16.59% of reference with a coverageData >= 22X There is a 15.42% of reference with a coverageData >= 23X There is a 14.39% of reference with a coverageData >= 24X There is a 13.39% of reference with a coverageData >= 25X There is a 12.5% of reference with a coverageData >= 26X There is a 11.64% of reference with a coverageData >= 27X There is a 10.87% of reference with a coverageData >= 28X There is a 10.13% of reference with a coverageData >= 29X There is a 9.47% of reference with a coverageData >= 30X There is a 8.83% of reference with a coverageData >= 31X There is a 8.27% of reference with a coverageData >= 32X There is a 7.72% of reference with a coverageData >= 33X There is a 7.23% of reference with a coverageData >= 34X There is a 6.76% of reference with a coverageData >= 35X There is a 6.34% of reference with a coverageData >= 36X There is a 5.94% of reference with a coverageData >= 37X There is a 5.58% of reference with a coverageData >= 38X There is a 5.22% of reference with a coverageData >= 39X There is a 4.91% of reference with a coverageData >= 40X There is a 4.61% of reference with a coverageData >= 41X There is a 4.34% of reference with a coverageData >= 42X There is a 4.08% of reference with a coverageData >= 43X There is a 3.84% of reference with a coverageData >= 44X There is a 3.61% of reference with a coverageData >= 45X There is a 3.41% of reference with a coverageData >= 46X There is a 3.21% of reference with a coverageData >= 47X There is a 3.03% of reference with a coverageData >= 48X There is a 2.86% of reference with a coverageData >= 49X There is a 2.7% of reference with a coverageData >= 50X There is a 2.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2947819892 11.826730381546371 372.76978574040425 chr2 243199373 3067773102 12.614231131262004 80.48125864327992 chr3 198022430 2374461406 11.99087096345601 22.458458678756873 chr4 191154276 2424097443 12.6813665575548 83.68149861694214 chr5 180915260 2205916334 12.193091583319173 17.41458021903109 chr6 171115067 2102158329 12.285056867610612 48.119062842440975 chr7 159138663 1960049739 12.31661559831001 98.20718687520494 chr8 146364022 1823388348 12.45789998856413 45.54816989570494 chr9 141213431 1507695483 10.676714476259699 120.06727641688146 chr10 135534747 1899970764 14.018329661249156 262.4432928093579 chr11 135006516 1648103171 12.207582417725675 71.1061263760061 chr12 133851895 1577595359 11.786126442214359 25.350749218632984 chr13 115169878 1178456333 10.232331174302365 14.849834078234498 chr14 107349540 1080877226 10.06876439340122 17.767964743975497 chr15 102531392 991940973 9.67450995886216 16.98772860498297 chr16 90354753 1022835606 11.320219158808392 44.331931315400816 chr17 81195210 961385501 11.840421386926643 62.21859322225182 chr18 78077248 1012076885 12.962507144206722 143.7195431844587 chr19 59128983 685159627 11.587542897533009 178.20225715525697 chr20 63025520 727148426 11.537364959464039 25.76902735386109 chr21 48129895 506004977 10.513319777655862 44.94646902005437 chr22 51304566 417552457 8.138699721190507 31.739619172809686 chrMT 16571 31731463 1914.8791865306862 401.1776323107019 chrX 155270560 983711397 6.335466278990686 27.54954189799758 chrY 59373566 380260671 6.40454492829351 140.16905322536144