BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617399.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,632,280 (92.6%) number of supplementary alignments = 471,376 (1.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,958,640 number of mapped paired reads (second in pair) = 14,673,640 number of mapped paired reads (both in pair) = 29,020,774 number of mapped paired reads (singletons) = 611,506 number of mapped bases = 2,909,869,946 bp number of sequenced bases = 2,909,229,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,379,218 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 61,304.6603 std insert size = 2,374,418.0534 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.8309 >>>>>>> ACTG content number of A's = 867,110,657 bp (29.81%) number of C's = 585,219,377 bp (20.12%) number of T's = 859,083,208 bp (29.53%) number of G's = 597,343,074 bp (20.53%) number of N's = 473,137 bp (0.02%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 30,462,655 number of insertions = 258,865 mapped reads with insertion percentage = 0.86% number of deletions = 285,246 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.94X std coverageData = 2.8932X There is a 29.44% of reference with a coverageData >= 1X There is a 16.8% of reference with a coverageData >= 2X There is a 10.72% of reference with a coverageData >= 3X There is a 7.4% of reference with a coverageData >= 4X There is a 5.36% of reference with a coverageData >= 5X There is a 4.03% of reference with a coverageData >= 6X There is a 3.11% of reference with a coverageData >= 7X There is a 2.46% of reference with a coverageData >= 8X There is a 1.98% of reference with a coverageData >= 9X There is a 1.61% of reference with a coverageData >= 10X There is a 1.33% of reference with a coverageData >= 11X There is a 1.12% of reference with a coverageData >= 12X There is a 0.94% of reference with a coverageData >= 13X There is a 0.81% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.6% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.46% of reference with a coverageData >= 18X There is a 0.4% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187208063 0.7510836372199049 2.705705862235914 chr2 243199373 290168529 1.1931302512034025 3.0853954661446936 chr3 198022430 245337216 1.2389364982542634 3.36877989769851 chr4 191154276 139338767 0.7289335604504081 2.2399345351360784 chr5 180915260 186054343 1.0284060227976346 2.824561011025764 chr6 171115067 133183521 0.7783272585809173 2.55837406190611 chr7 159138663 217984817 1.3697791152109906 3.196638421368957 chr8 146364022 129107726 0.8821001516342588 3.21917975765988 chr9 141213431 116033789 0.8216908843465464 2.5619372584332516 chr10 135534747 93298866 0.6883759926153844 2.3852699795108223 chr11 135006516 216160928 1.6011147787859366 3.7910889924045903 chr12 133851895 138474233 1.0345332279382373 2.784657931077249 chr13 115169878 125776253 1.092093307592112 2.732629436102076 chr14 107349540 84386345 0.7860894885995785 2.8538705596839966 chr15 102531392 66832472 0.6518244870800155 2.3548390541664617 chr16 90354753 73611648 0.8146959131192578 3.2907680013490865 chr17 81195210 90314931 1.1123184606579624 3.634375048708025 chr18 78077248 41611678 0.5329552342828476 1.979419001905936 chr19 59128983 41988254 0.7101129068971134 2.3217478422182993 chr20 63025520 99400065 1.5771399426771886 4.699098629465898 chr21 48129895 39790639 0.8267343820301291 2.4852107975796187 chr22 51304566 23667864 0.46132081109505924 2.0640314090885465 chrMT 16571 184378 11.126546376199384 5.23560765225454 chrX 155270560 127626696 0.8219632620633299 2.530950726522455 chrY 59373566 2327925 0.03920810483237608 0.6083832819880527