BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068143.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 = 4,594,241 number of mapped reads = 4,359,726 (94.9%) number of supplementary alignments = 29,800 (0.65%) number of secondary alignments = 0 number of mapped bases = 282,470,709 bp number of sequenced bases = 282,343,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 463,807 duplication rate = 8.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2921 >>>>>>> ACTG content number of A's = 75,401,822 bp (26.71%) number of C's = 50,724,855 bp (17.97%) number of T's = 91,800,187 bp (32.51%) number of G's = 64,384,079 bp (22.8%) number of N's = 32,528 bp (0.01%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,667,466 number of insertions = 18,363 mapped reads with insertion percentage = 0.42% number of deletions = 71,520 mapped reads with deletion percentage = 1.62% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0912X std coverageData = 0.8937X There is a 6.77% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 27091493 0.10869177734165003 2.0242578618865616 chr2 243199373 25139734 0.10337088327937424 0.9451269817259464 chr3 198022430 20849494 0.10528854736304367 0.4165957260437394 chr4 191154276 14419821 0.07543551366855115 0.41371865156682125 chr5 180915260 13676281 0.07559495533986464 0.3603530199854728 chr6 171115067 18156271 0.10610562423471452 0.5229037138641184 chr7 159138663 22551658 0.14171074190814334 1.4482846763618134 chr8 146364022 11004752 0.0751875484810058 1.225333081368623 chr9 141213431 12483193 0.08839947384324937 0.6717951143166646 chr10 135534747 13740894 0.10138281366327412 0.6369050566450823 chr11 135006516 12596705 0.09330442243246985 0.5693063451281686 chr12 133851895 12416590 0.09276364746274231 0.43017017362418264 chr13 115169878 7303312 0.06341338661485775 0.33308936431180103 chr14 107349540 6080768 0.05664456503493168 0.3905438171022804 chr15 102531392 5908698 0.0576281847417033 0.34801488689706384 chr16 90354753 5892502 0.06521518574678634 0.38528492112302354 chr17 81195210 7821059 0.0963241427665499 0.44585083367999784 chr18 78077248 7411856 0.09492978031192903 1.1715239078779844 chr19 59128983 5678169 0.09603021584186557 1.256028237585858 chr20 63025520 4355482 0.06910664124627611 0.3796221636855163 chr21 48129895 4089181 0.08496135302185887 0.41279491017271325 chr22 51304566 2430702 0.047377888354030714 0.27481546051429806 chrMT 16571 273588 16.51004767364673 10.151293586016338 chrX 155270560 20205888 0.1301334135717679 0.5495877492350024 chrY 59373566 892618 0.015033929408922482 0.36634880026272737