BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975208.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 33,099,416 number of mapped reads = 33,028,764 (99.79%) number of supplementary alignments = 59,386 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,516,707 number of mapped paired reads (second in pair) = 16,512,057 number of mapped paired reads (both in pair) = 32,981,992 number of mapped paired reads (singletons) = 46,772 number of mapped bases = 3,122,167,843 bp number of sequenced bases = 3,121,095,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,286,002 duplication rate = 45.64% >>>>>>> Insert size mean insert size = 121,215.5735 std insert size = 3,375,856.6201 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 55.9871 >>>>>>> ACTG content number of A's = 865,894,841 bp (27.74%) number of C's = 660,838,759 bp (21.17%) number of T's = 901,354,448 bp (28.88%) number of G's = 692,861,494 bp (22.2%) number of N's = 145,755 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 21,809,748 number of insertions = 325,069 mapped reads with insertion percentage = 0.97% number of deletions = 721,494 mapped reads with deletion percentage = 2.15% homopolymer indels = 47.79% >>>>>>> Coverage mean coverageData = 1.0086X std coverageData = 17.7167X There is a 6.44% of reference with a coverageData >= 1X There is a 3.26% of reference with a coverageData >= 2X There is a 2.14% of reference with a coverageData >= 3X There is a 1.73% of reference with a coverageData >= 4X There is a 1.51% of reference with a coverageData >= 5X There is a 1.38% of reference with a coverageData >= 6X There is a 1.29% of reference with a coverageData >= 7X There is a 1.22% of reference with a coverageData >= 8X There is a 1.15% of reference with a coverageData >= 9X There is a 1.1% of reference with a coverageData >= 10X There is a 1.06% of reference with a coverageData >= 11X There is a 1.02% of reference with a coverageData >= 12X There is a 0.98% of reference with a coverageData >= 13X There is a 0.94% of reference with a coverageData >= 14X There is a 0.91% of reference with a coverageData >= 15X There is a 0.88% of reference with a coverageData >= 16X There is a 0.86% of reference with a coverageData >= 17X There is a 0.83% of reference with a coverageData >= 18X There is a 0.81% of reference with a coverageData >= 19X There is a 0.79% of reference with a coverageData >= 20X There is a 0.77% of reference with a coverageData >= 21X There is a 0.75% of reference with a coverageData >= 22X There is a 0.73% of reference with a coverageData >= 23X There is a 0.71% of reference with a coverageData >= 24X There is a 0.7% of reference with a coverageData >= 25X There is a 0.68% of reference with a coverageData >= 26X There is a 0.66% of reference with a coverageData >= 27X There is a 0.65% of reference with a coverageData >= 28X There is a 0.64% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.61% of reference with a coverageData >= 31X There is a 0.6% of reference with a coverageData >= 32X There is a 0.59% of reference with a coverageData >= 33X There is a 0.57% of reference with a coverageData >= 34X There is a 0.56% of reference with a coverageData >= 35X There is a 0.55% of reference with a coverageData >= 36X There is a 0.54% of reference with a coverageData >= 37X There is a 0.53% of reference with a coverageData >= 38X There is a 0.52% of reference with a coverageData >= 39X There is a 0.51% of reference with a coverageData >= 40X There is a 0.51% of reference with a coverageData >= 41X There is a 0.5% of reference with a coverageData >= 42X There is a 0.49% of reference with a coverageData >= 43X There is a 0.48% of reference with a coverageData >= 44X There is a 0.47% of reference with a coverageData >= 45X There is a 0.47% of reference with a coverageData >= 46X There is a 0.46% of reference with a coverageData >= 47X There is a 0.45% of reference with a coverageData >= 48X There is a 0.44% of reference with a coverageData >= 49X There is a 0.44% of reference with a coverageData >= 50X There is a 0.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 321069820 1.2881405017642864 20.018656629090245 chr2 243199373 267252390 1.0989024630421231 18.316799843362574 chr3 198022430 210272111 1.0618600680741066 17.107811748339568 chr4 191154276 161188778 0.8432391959675545 14.842783966747614 chr5 180915260 157114454 0.8684422419645529 14.760561796118118 chr6 171115067 198096495 1.1576800247519992 19.84221697354084 chr7 159138663 168796919 1.0606908203068164 19.68685964322731 chr8 146364022 126635292 0.8652077899307796 14.55203382786867 chr9 141213431 135957046 0.9627770180019208 18.158518809738712 chr10 135534747 146642225 1.0819529917298625 19.07965545964674 chr11 135006516 185694553 1.3754488190777399 21.436723709555004 chr12 133851895 165213898 1.2343037653669378 18.761395576741368 chr13 115169878 83852279 0.7280747401677372 16.566331981857516 chr14 107349540 104318918 0.9717686540622344 17.98729681997914 chr15 102531392 109312716 1.0661390025798148 16.996353348322852 chr16 90354753 86143424 0.9533911735667077 16.481168947175533 chr17 81195210 112365962 1.3838989024106225 19.066666268029678 chr18 78077248 56704470 0.7262611253921245 14.884624445625143 chr19 59128983 95492660 1.6149890486024425 26.64212951019456 chr20 63025520 66489118 1.0549554846988967 19.531354394468227 chr21 48129895 33741322 0.7010470727185255 15.776544821833143 chr22 51304566 43061570 0.8393321171452849 16.82896184346218 chrMT 16571 19077 1.1512280490012672 3.2552714351074243 chrX 155270560 85518201 0.5507689352057467 12.796614942636284 chrY 59373566 1214145 0.020449251776455537 1.5066534706916728