BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472782.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,460,250 number of mapped reads = 14,342,442 (99.19%) number of supplementary alignments = 56,046 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,190,561 number of mapped paired reads (second in pair) = 7,151,881 number of mapped paired reads (both in pair) = 14,274,658 number of mapped paired reads (singletons) = 67,784 number of mapped bases = 1,410,061,989 bp number of sequenced bases = 1,409,871,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,142,716 duplication rate = 46.15% >>>>>>> Insert size mean insert size = 25,020.067 std insert size = 1,587,861.4537 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.8765 >>>>>>> ACTG content number of A's = 387,823,447 bp (27.51%) number of C's = 318,746,338 bp (22.61%) number of T's = 385,265,913 bp (27.33%) number of G's = 317,761,443 bp (22.54%) number of N's = 274,333 bp (0.02%) GC percentage = 45.15% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,112,869 number of insertions = 81,826 mapped reads with insertion percentage = 0.56% number of deletions = 76,726 mapped reads with deletion percentage = 0.53% homopolymer indels = 43.42% >>>>>>> Coverage mean coverageData = 0.4555X std coverageData = 18.0139X There is a 4.13% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 176182286 0.7068479319856941 30.082809778736696 chr2 243199373 116487170 0.4789780851943233 17.852101371218584 chr3 198022430 181631531 0.9172270585710922 24.029062230769973 chr4 191154276 67462813 0.3529233790197819 19.7922440748066 chr5 180915260 57353170 0.3170167624334177 11.04285007400916 chr6 171115067 85935236 0.5022073012425025 19.2486386659119 chr7 159138663 49975838 0.31403957440562386 10.13186897299177 chr8 146364022 65726138 0.4490593870124722 15.734860267975595 chr9 141213431 89915674 0.6367359914936137 17.79376737464605 chr10 135534747 30054622 0.22174846425175385 10.176084445464351 chr11 135006516 68157346 0.5048448624509353 18.41595933887932 chr12 133851895 50738065 0.3790612377956995 12.034777913365144 chr13 115169878 38089975 0.33072862159322597 15.529397829365934 chr14 107349540 40321787 0.37561210788607013 14.533083722906223 chr15 102531392 22660075 0.2210062163205587 7.36349175312205 chr16 90354753 46230464 0.5116550315842266 16.50920554734179 chr17 81195210 58412840 0.7194123889820594 20.647926302041533 chr18 78077248 21110664 0.2703817634555972 13.174477951861348 chr19 59128983 27484412 0.46482132121230635 12.604722369749963 chr20 63025520 22690730 0.3600244789729621 12.592008230801364 chr21 48129895 5735309 0.11916313135526267 6.589106030814602 chr22 51304566 8957827 0.17460097021384022 7.370460220434252 chrMT 16571 1138 0.0686741898497375 0.30004613850253387 chrX 155270560 77256240 0.4975588418049114 25.007022078818856 chrY 59373566 1490639 0.025106105299452623 0.6063978720133895