BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082954.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 = 1,424,376 number of mapped reads = 1,262,700 (88.65%) number of supplementary alignments = 11,952 (0.84%) number of secondary alignments = 0 number of mapped bases = 82,011,302 bp number of sequenced bases = 81,982,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,677 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.94 >>>>>>> ACTG content number of A's = 22,761,443 bp (27.76%) number of C's = 15,785,545 bp (19.25%) number of T's = 24,311,381 bp (29.65%) number of G's = 19,120,687 bp (23.32%) number of N's = 3,455 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 654,868 number of insertions = 6,660 mapped reads with insertion percentage = 0.52% number of deletions = 17,124 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2807X There is a 2.43% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 7789436 0.03125142063337126 0.5417353010716157 chr2 243199373 8051116 0.03310500311199404 0.3518441154393261 chr3 198022430 5718462 0.02887784984761575 0.17880222459065243 chr4 191154276 4670496 0.02443312332704501 0.17485985455600953 chr5 180915260 4368915 0.024148957915435105 0.1662667956946842 chr6 171115067 5492532 0.03209847090788329 0.25321034192758063 chr7 159138663 4325038 0.027177795253941525 0.3128831038176084 chr8 146364022 6528311 0.044603249560879105 0.29490031567562025 chr9 141213431 2507145 0.017754295623622372 0.23953703980280242 chr10 135534747 3034662 0.022390287857327097 0.1890667145275475 chr11 135006516 3387968 0.02509484801459509 0.2810397123439674 chr12 133851895 2634468 0.019681962664779607 0.1542469491428229 chr13 115169878 1789235 0.015535616005428085 0.13032595638996558 chr14 107349540 1804606 0.016810561088571038 0.15687388445879769 chr15 102531392 1668007 0.016268256652557687 0.14210135293645118 chr16 90354753 3300663 0.036530042863378756 0.21864855654616785 chr17 81195210 2211766 0.02724010443473205 0.20498223374992564 chr18 78077248 2822030 0.03614407618465241 0.5469104907643548 chr19 59128983 1575043 0.026637410624836894 0.3655836636742561 chr20 63025520 1704130 0.027038729708219782 0.18679301256714922 chr21 48129895 1728715 0.03591769730642463 0.2053351897305843 chr22 51304566 1194571 0.023283912001126762 0.16052406708833278 chrMT 16571 72513 4.375897652525496 3.2823990799610967 chrX 155270560 3471406 0.022357142268308944 0.18362778355765177 chrY 59373566 160068 0.0026959472166451985 0.06511255922478573