BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432723.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 408,567,090 number of mapped reads = 408,411,285 (99.96%) number of supplementary alignments = 3,053,422 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 204,209,931 number of mapped paired reads (second in pair) = 204,201,354 number of mapped paired reads (both in pair) = 408,354,920 number of mapped paired reads (singletons) = 56,365 number of mapped bases = 56,186,318,246 bp number of sequenced bases = 56,131,511,812 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,320,590 duplication rate = 32.67% >>>>>>> Insert size mean insert size = 76,362.0176 std insert size = 2,747,215.6067 median insert size = 321 >>>>>>> Mapping quality mean mapping quality = 57.4199 >>>>>>> ACTG content number of A's = 15,543,982,748 bp (27.69%) number of C's = 11,869,996,855 bp (21.15%) number of T's = 15,321,771,118 bp (27.3%) number of G's = 13,385,769,542 bp (23.85%) number of N's = 9,991,549 bp (0.02%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 491,865,989 number of insertions = 11,738,387 mapped reads with insertion percentage = 2.82% number of deletions = 38,504,616 mapped reads with deletion percentage = 8.99% homopolymer indels = 52.59% >>>>>>> Coverage mean coverageData = 18.1498X std coverageData = 51.7193X There is a 56.15% of reference with a coverageData >= 1X There is a 48.95% of reference with a coverageData >= 2X There is a 44.19% of reference with a coverageData >= 3X There is a 40.69% of reference with a coverageData >= 4X There is a 37.84% of reference with a coverageData >= 5X There is a 35.46% of reference with a coverageData >= 6X There is a 33.41% of reference with a coverageData >= 7X There is a 31.62% of reference with a coverageData >= 8X There is a 30.04% of reference with a coverageData >= 9X There is a 28.63% of reference with a coverageData >= 10X There is a 27.36% of reference with a coverageData >= 11X There is a 26.2% of reference with a coverageData >= 12X There is a 25.15% of reference with a coverageData >= 13X There is a 24.18% of reference with a coverageData >= 14X There is a 23.28% of reference with a coverageData >= 15X There is a 22.45% of reference with a coverageData >= 16X There is a 21.68% of reference with a coverageData >= 17X There is a 20.95% of reference with a coverageData >= 18X There is a 20.28% of reference with a coverageData >= 19X There is a 19.64% of reference with a coverageData >= 20X There is a 19.04% of reference with a coverageData >= 21X There is a 18.48% of reference with a coverageData >= 22X There is a 17.94% of reference with a coverageData >= 23X There is a 17.43% of reference with a coverageData >= 24X There is a 16.95% of reference with a coverageData >= 25X There is a 16.5% of reference with a coverageData >= 26X There is a 16.06% of reference with a coverageData >= 27X There is a 15.65% of reference with a coverageData >= 28X There is a 15.25% of reference with a coverageData >= 29X There is a 14.87% of reference with a coverageData >= 30X There is a 14.51% of reference with a coverageData >= 31X There is a 14.16% of reference with a coverageData >= 32X There is a 13.82% of reference with a coverageData >= 33X There is a 13.5% of reference with a coverageData >= 34X There is a 13.19% of reference with a coverageData >= 35X There is a 12.9% of reference with a coverageData >= 36X There is a 12.61% of reference with a coverageData >= 37X There is a 12.33% of reference with a coverageData >= 38X There is a 12.07% of reference with a coverageData >= 39X There is a 11.81% of reference with a coverageData >= 40X There is a 11.56% of reference with a coverageData >= 41X There is a 11.32% of reference with a coverageData >= 42X There is a 11.09% of reference with a coverageData >= 43X There is a 10.87% of reference with a coverageData >= 44X There is a 10.65% of reference with a coverageData >= 45X There is a 10.44% of reference with a coverageData >= 46X There is a 10.24% of reference with a coverageData >= 47X There is a 10.04% of reference with a coverageData >= 48X There is a 9.85% of reference with a coverageData >= 49X There is a 9.67% of reference with a coverageData >= 50X There is a 9.49% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4501979241 18.062058272665247 51.26639326854807 chr2 243199373 3899089084 16.032480001500662 48.40983807185906 chr3 198022430 3121057626 15.76113183743882 43.27559350677652 chr4 191154276 2515243606 13.158186458774273 38.493944949330064 chr5 180915260 3838690278 21.218167433747713 55.988498820926495 chr6 171115067 3391871860 19.822169487856964 53.42981934539121 chr7 159138663 2734335666 17.182095252364913 47.31621682986647 chr8 146364022 2874856398 19.641824259243162 51.360112179316815 chr9 141213431 2252911798 15.953948445597927 47.73092230559318 chr10 135534747 3876312376 28.600137321243533 70.88394268773615 chr11 135006516 2890553901 21.410476965422912 56.43828870638694 chr12 133851895 3274527000 24.46380755386392 63.22987561565409 chr13 115169878 1325950697 11.512999058660112 36.885053616021196 chr14 107349540 1751556155 16.316382492183944 47.12966903002964 chr15 102531392 1674190909 16.328569000604226 48.126086740046674 chr16 90354753 2210580627 24.46557102535602 66.97719557213244 chr17 81195210 1849123880 22.7738050064776 58.433565813324414 chr18 78077248 1619541627 20.74281136292099 55.74430676647334 chr19 59128983 1475395247 24.952149895762624 65.53642520622031 chr20 63025520 1805679445 28.649972979199536 68.20332447969813 chr21 48129895 734337196 15.257402826247596 47.595899805600325 chr22 51304566 1104502143 21.528340050669176 62.15336277302786 chrMT 16571 4428694 267.2556876470943 432.4347248551679 chrX 155270560 1398041878 9.003908261810867 28.215421791919177 chrY 59373566 61560914 1.0368404350178326 13.804098093700441