BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084262.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,919,108 number of mapped reads = 1,649,667 (85.96%) number of supplementary alignments = 11,125 (0.58%) number of secondary alignments = 0 number of mapped bases = 106,674,481 bp number of sequenced bases = 106,636,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,521 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9614 >>>>>>> ACTG content number of A's = 30,597,688 bp (28.69%) number of C's = 20,116,736 bp (18.86%) number of T's = 32,531,315 bp (30.51%) number of G's = 23,389,364 bp (21.93%) number of N's = 1,264 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 911,805 number of insertions = 8,402 mapped reads with insertion percentage = 0.51% number of deletions = 23,797 mapped reads with deletion percentage = 1.43% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.2677X There is a 3.09% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8363121 0.03355305983370047 0.3928099915392441 chr2 243199373 9081936 0.03734358311853049 0.3383633410189267 chr3 198022430 7585173 0.038304615290298175 0.2126839561988756 chr4 191154276 6310868 0.033014526967735734 0.2036334892319942 chr5 180915260 6369402 0.03520654918772469 0.20583203008685905 chr6 171115067 6600694 0.038574592616090315 0.24155710059580265 chr7 159138663 5745428 0.0361032818278736 0.31603933562187186 chr8 146364022 5355036 0.036587106085401236 0.27575505733058064 chr9 141213431 4603353 0.032598549354699836 0.2547439935182967 chr10 135534747 4579145 0.03378576417750645 0.27043876122130406 chr11 135006516 4577048 0.03390242290231384 0.24354172496756468 chr12 133851895 5052541 0.03774725042181883 0.21251291776405357 chr13 115169878 3512567 0.030499007735338576 0.18986392158666257 chr14 107349540 3448487 0.03212391035862846 0.2046943283601464 chr15 102531392 3139011 0.030615121269396205 0.1941112795450325 chr16 90354753 3017694 0.03339828730426611 0.21611883449074482 chr17 81195210 2837861 0.0349510888634933 0.2281129891808295 chr18 78077248 2874039 0.036810198535686095 0.48801293862837714 chr19 59128983 2101657 0.035543601350288744 0.3142204128639769 chr20 63025520 2261214 0.03587775237713231 0.21189233890654074 chr21 48129895 1468714 0.030515628592167093 0.19646917989785814 chr22 51304566 1147048 0.022357620177510126 0.1614982176247825 chrMT 16571 9912 0.5981534005189789 0.9044605707823506 chrX 155270560 6376971 0.04107005861252771 0.2391544795112355 chrY 59373566 255561 0.004304289218538769 0.08987216112552038