BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124789.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 547,858 number of mapped reads = 546,888 (99.82%) number of supplementary alignments = 257,830 (47.06%) number of secondary alignments = 0 number of mapped bases = 83,002,429 bp number of sequenced bases = 82,954,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 801,457 duplication rate = 9.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1007 >>>>>>> ACTG content number of A's = 23,919,677 bp (28.83%) number of C's = 12,255,374 bp (14.77%) number of T's = 27,832,803 bp (33.55%) number of G's = 18,946,632 bp (22.84%) number of N's = 0 bp (0%) GC percentage = 37.61% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 710,300 number of insertions = 17,684 mapped reads with insertion percentage = 3.18% number of deletions = 45,417 mapped reads with deletion percentage = 8.03% homopolymer indels = 87.18% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 84.0238X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 582973 0.0023389028988617844 2.008787298019857 chr2 243199373 39786 1.6359417176622408E-4 0.020231877877249976 chr3 198022430 26081 1.317073020465409E-4 0.011931490809243375 chr4 191154276 21029 1.1001061781113387E-4 0.010870360052656175 chr5 180915260 42216 2.333468166256401E-4 0.09034882944147421 chr6 171115067 42950 2.510006906639028E-4 0.13966004795069292 chr7 159138663 22991 1.4447149150674968E-4 0.012083680350668586 chr8 146364022 82039396 0.5605161355841943 386.4148147240418 chr9 141213431 17179 1.2165273429267504E-4 0.011313580789530842 chr10 135534747 21960 1.6202487174746415E-4 0.017629990775719622 chr11 135006516 16146 1.1959422758528189E-4 0.011170814510432012 chr12 133851895 26422 1.973972800310373E-4 0.05623598812595756 chr13 115169878 7597 6.596342838880145E-5 0.008412968960887153 chr14 107349540 11119 1.0357752813845314E-4 0.01017540463728195 chr15 102531392 9482 9.247899414064329E-5 0.009615648208501686 chr16 90354753 12959 1.434235562571899E-4 0.012954881834539144 chr17 81195210 14627 1.8014609482505187E-4 0.03497557783652373 chr18 78077248 5510 7.057113488426231E-5 0.008488336863132261 chr19 59128983 5921 1.0013701740819726E-4 0.010244362909876686 chr20 63025520 8876 1.408318408162281E-4 0.013656785545858325 chr21 48129895 3720 7.729083971614731E-5 0.008789999541897194 chr22 51304566 2837 5.5297222473336976E-5 0.007472611952510947 chrMT 16571 371 0.022388510047673647 0.1479434509044549 chrX 155270560 13815 8.897372431708883E-5 0.010686100520839953 chrY 59373566 6466 1.0890368282747242E-4 0.010890048045465502