BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231822.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,037,386 number of mapped reads = 500,477 (48.24%) number of supplementary alignments = 3,896 (0.38%) number of secondary alignments = 0 number of mapped bases = 31,735,480 bp number of sequenced bases = 31,715,591 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,360 duplication rate = 6.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6359 >>>>>>> ACTG content number of A's = 8,948,105 bp (28.21%) number of C's = 5,205,801 bp (16.41%) number of T's = 10,802,090 bp (34.06%) number of G's = 6,758,352 bp (21.31%) number of N's = 1,243 bp (0%) GC percentage = 37.72% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 301,015 number of insertions = 3,023 mapped reads with insertion percentage = 0.6% number of deletions = 11,383 mapped reads with deletion percentage = 2.24% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.0103X std coverageData = 0.248X There is a 0.81% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.04% 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 1750771 0.007024138968945638 0.1245503966900419 chr2 243199373 1703019 0.007002563283746624 0.13769085803446862 chr3 198022430 3341580 0.016874755046688398 0.16053530820691234 chr4 191154276 1058924 0.005539630199012655 0.09458308858762283 chr5 180915260 1736387 0.009597791805953793 0.12176599913371246 chr6 171115067 1401974 0.008193165129053189 0.12668938345973368 chr7 159138663 2024721 0.012722998684486874 0.17638142321062575 chr8 146364022 1958346 0.013379968473399836 0.937482972546557 chr9 141213431 886573 0.006278248419585528 0.11008960986047057 chr10 135534747 1672322 0.012338695699929996 0.14778562223380698 chr11 135006516 1734522 0.012847690995892376 0.15147375790076367 chr12 133851895 1196972 0.008942510675698689 0.13330966420310694 chr13 115169878 644179 0.005593294107683261 0.09463233826389862 chr14 107349540 2599096 0.02421152433443124 0.19894871266931377 chr15 102531392 583747 0.005693349018415745 0.11218503018593277 chr16 90354753 719681 0.007965059679815626 0.1116202698796 chr17 81195210 753490 0.009279980924983137 0.12006794468933588 chr18 78077248 1532470 0.019627612899471045 0.3579276158165598 chr19 59128983 436760 0.007386563709374132 0.11372969295965997 chr20 63025520 924985 0.014676356498129647 0.14865826736180407 chr21 48129895 580421 0.01205946948357149 0.13896405939314888 chr22 51304566 344389 0.006712638403373298 0.0987268250709246 chrMT 16571 26813 1.6180677086476374 1.7170770483699627 chrX 155270560 1996756 0.012859849285015781 0.14267067961156862 chrY 59373566 126582 0.0021319588585937384 0.058013824911883456