BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038434.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 78,963,578 number of mapped reads = 78,598,645 (99.54%) number of supplementary alignments = 106,508 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 39,418,584 number of mapped paired reads (second in pair) = 39,180,061 number of mapped paired reads (both in pair) = 78,323,716 number of mapped paired reads (singletons) = 274,929 number of mapped bases = 11,680,704,346 bp number of sequenced bases = 11,678,826,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,374,351 duplication rate = 36.62% >>>>>>> Insert size mean insert size = 20,743.682 std insert size = 1,510,183.7769 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.7267 >>>>>>> ACTG content number of A's = 2,951,596,002 bp (25.27%) number of C's = 2,886,638,984 bp (24.72%) number of T's = 2,972,664,134 bp (25.45%) number of G's = 2,866,740,537 bp (24.55%) number of N's = 1,186,385 bp (0.01%) GC percentage = 49.26% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 62,270,970 number of insertions = 556,824 mapped reads with insertion percentage = 0.68% number of deletions = 677,166 mapped reads with deletion percentage = 0.84% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 3.7732X std coverageData = 23.6034X There is a 23.76% of reference with a coverageData >= 1X There is a 14.71% of reference with a coverageData >= 2X There is a 9.3% of reference with a coverageData >= 3X There is a 7.18% of reference with a coverageData >= 4X There is a 5.73% of reference with a coverageData >= 5X There is a 4.98% of reference with a coverageData >= 6X There is a 4.48% of reference with a coverageData >= 7X There is a 4.17% of reference with a coverageData >= 8X There is a 3.95% of reference with a coverageData >= 9X There is a 3.79% of reference with a coverageData >= 10X There is a 3.66% of reference with a coverageData >= 11X There is a 3.56% of reference with a coverageData >= 12X There is a 3.48% of reference with a coverageData >= 13X There is a 3.4% of reference with a coverageData >= 14X There is a 3.34% of reference with a coverageData >= 15X There is a 3.27% of reference with a coverageData >= 16X There is a 3.22% of reference with a coverageData >= 17X There is a 3.16% of reference with a coverageData >= 18X There is a 3.11% of reference with a coverageData >= 19X There is a 3.07% of reference with a coverageData >= 20X There is a 3.02% of reference with a coverageData >= 21X There is a 2.98% of reference with a coverageData >= 22X There is a 2.94% of reference with a coverageData >= 23X There is a 2.9% of reference with a coverageData >= 24X There is a 2.86% of reference with a coverageData >= 25X There is a 2.82% of reference with a coverageData >= 26X There is a 2.78% of reference with a coverageData >= 27X There is a 2.75% of reference with a coverageData >= 28X There is a 2.71% of reference with a coverageData >= 29X There is a 2.68% of reference with a coverageData >= 30X There is a 2.65% of reference with a coverageData >= 31X There is a 2.62% of reference with a coverageData >= 32X There is a 2.59% of reference with a coverageData >= 33X There is a 2.56% of reference with a coverageData >= 34X There is a 2.53% of reference with a coverageData >= 35X There is a 2.5% of reference with a coverageData >= 36X There is a 2.47% of reference with a coverageData >= 37X There is a 2.44% of reference with a coverageData >= 38X There is a 2.41% of reference with a coverageData >= 39X There is a 2.39% of reference with a coverageData >= 40X There is a 2.36% of reference with a coverageData >= 41X There is a 2.33% of reference with a coverageData >= 42X There is a 2.31% of reference with a coverageData >= 43X There is a 2.28% of reference with a coverageData >= 44X There is a 2.26% of reference with a coverageData >= 45X There is a 2.23% of reference with a coverageData >= 46X There is a 2.21% of reference with a coverageData >= 47X There is a 2.18% of reference with a coverageData >= 48X There is a 2.16% of reference with a coverageData >= 49X There is a 2.14% of reference with a coverageData >= 50X There is a 2.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1188155715 4.7669117542539645 27.497832057483055 chr2 243199373 876500994 3.604042984107529 23.990815605465528 chr3 198022430 677221932 3.4199253690604645 21.963287175371505 chr4 191154276 420369325 2.199110235964588 16.46941806593203 chr5 180915260 574421969 3.1750885414530536 21.913185166241462 chr6 171115067 602238005 3.519491389966262 22.711722308933506 chr7 159138663 566388162 3.55908583949835 22.751415060764515 chr8 146364022 445650467 3.0448088328701433 21.091987473030677 chr9 141213431 477021334 3.3780167411979387 21.99740518179379 chr10 135534747 460273503 3.395981570689028 21.104781255844927 chr11 135006516 680321082 5.039172198177456 28.40952242942996 chr12 133851895 620762641 4.637682873298133 25.749110266898803 chr13 115169878 229849109 1.995739797518931 16.425993759403976 chr14 107349540 398152803 3.708938137974322 23.423508017606725 chr15 102531392 423346812 4.128948254208819 23.97609060519954 chr16 90354753 488222960 5.403400969952295 28.345451040960615 chr17 81195210 631095148 7.772566238821231 33.05889148979473 chr18 78077248 224480758 2.8751110438728578 23.358319540111445 chr19 59128983 663016948 11.213061925993214 40.28991180210406 chr20 63025520 311274159 4.93885903678383 27.747926877798506 chr21 48129895 124339148 2.5834078383092254 22.05635097726068 chr22 51304566 204951063 3.99479186706306 20.904601054225857 chrMT 16571 1041185 62.83175426950697 22.824466431878736 chrX 155270560 386390491 2.4884980836032278 17.676240283857084 chrY 59373566 5218633 0.08789488911614303 2.283271798337446