BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975275.sorted.bam outfile = /mainsd/zhouyj/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 = 54,051,448 number of mapped reads = 53,901,893 (99.72%) number of supplementary alignments = 118,733 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,947,080 number of mapped paired reads (second in pair) = 26,954,813 number of mapped paired reads (both in pair) = 53,844,292 number of mapped paired reads (singletons) = 57,601 number of mapped bases = 4,942,575,919 bp number of sequenced bases = 4,940,839,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,352,608 duplication rate = 43.57% >>>>>>> Insert size mean insert size = 42,519.7758 std insert size = 2,049,446.7523 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 55.8911 >>>>>>> ACTG content number of A's = 1,278,200,900 bp (25.87%) number of C's = 1,104,700,473 bp (22.36%) number of T's = 1,332,178,111 bp (26.96%) number of G's = 1,225,605,861 bp (24.81%) number of N's = 154,152 bp (0%) GC percentage = 47.16% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 31,851,357 number of insertions = 505,690 mapped reads with insertion percentage = 0.93% number of deletions = 1,218,852 mapped reads with deletion percentage = 2.23% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 1.5966X std coverageData = 22.8913X There is a 11.7% of reference with a coverageData >= 1X There is a 5.98% of reference with a coverageData >= 2X There is a 3.54% of reference with a coverageData >= 3X There is a 2.74% of reference with a coverageData >= 4X There is a 2.25% of reference with a coverageData >= 5X There is a 2.02% of reference with a coverageData >= 6X There is a 1.85% of reference with a coverageData >= 7X There is a 1.73% of reference with a coverageData >= 8X There is a 1.64% of reference with a coverageData >= 9X There is a 1.57% of reference with a coverageData >= 10X There is a 1.5% of reference with a coverageData >= 11X There is a 1.45% of reference with a coverageData >= 12X There is a 1.4% of reference with a coverageData >= 13X There is a 1.35% of reference with a coverageData >= 14X There is a 1.31% of reference with a coverageData >= 15X There is a 1.27% of reference with a coverageData >= 16X There is a 1.24% of reference with a coverageData >= 17X There is a 1.21% of reference with a coverageData >= 18X There is a 1.17% of reference with a coverageData >= 19X There is a 1.15% of reference with a coverageData >= 20X There is a 1.12% of reference with a coverageData >= 21X There is a 1.09% of reference with a coverageData >= 22X There is a 1.07% of reference with a coverageData >= 23X There is a 1.04% of reference with a coverageData >= 24X There is a 1.02% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.98% of reference with a coverageData >= 27X There is a 0.96% of reference with a coverageData >= 28X There is a 0.94% of reference with a coverageData >= 29X There is a 0.92% of reference with a coverageData >= 30X There is a 0.9% of reference with a coverageData >= 31X There is a 0.89% of reference with a coverageData >= 32X There is a 0.87% of reference with a coverageData >= 33X There is a 0.86% of reference with a coverageData >= 34X There is a 0.84% of reference with a coverageData >= 35X There is a 0.83% of reference with a coverageData >= 36X There is a 0.81% of reference with a coverageData >= 37X There is a 0.8% of reference with a coverageData >= 38X There is a 0.79% of reference with a coverageData >= 39X There is a 0.77% of reference with a coverageData >= 40X There is a 0.76% of reference with a coverageData >= 41X There is a 0.75% of reference with a coverageData >= 42X There is a 0.74% of reference with a coverageData >= 43X There is a 0.73% of reference with a coverageData >= 44X There is a 0.71% of reference with a coverageData >= 45X There is a 0.7% of reference with a coverageData >= 46X There is a 0.69% of reference with a coverageData >= 47X There is a 0.68% of reference with a coverageData >= 48X There is a 0.67% of reference with a coverageData >= 49X There is a 0.66% of reference with a coverageData >= 50X There is a 0.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 598067729 2.3994633457703602 30.62330860033053 chr2 243199373 345542329 1.420819160582293 18.65358914863341 chr3 198022430 250177304 1.2633786182706677 18.029746713605622 chr4 191154276 210375357 1.100552712720902 16.71190301839683 chr5 180915260 237606473 1.3133578284109366 18.367714542660917 chr6 171115067 460776551 2.692787719271968 40.45851702915127 chr7 159138663 254781013 1.6010000850641808 23.583843565761303 chr8 146364022 169017932 1.1547778592747335 16.711221558012085 chr9 141213431 202977708 1.4373824540811562 20.061803590607944 chr10 135534747 209710374 1.5472812591740774 20.303045152700033 chr11 135006516 227259106 1.6833195369622012 21.575921693604617 chr12 133851895 276999394 2.069446936108002 25.692117131811873 chr13 115169878 97362643 0.8453828786724945 15.5077274061024 chr14 107349540 162701838 1.5156267833099237 21.132624122576708 chr15 102531392 175482478 1.7115000057738414 22.26085226128378 chr16 90354753 157941986 1.7480207820389924 21.588499998391217 chr17 81195210 206039931 2.5375872665394916 26.28090819445446 chr18 78077248 86525324 1.108201508331851 17.85253878956078 chr19 59128983 223938689 3.7872914032700344 38.683872949003714 chr20 63025520 131912243 2.092997296967958 27.25312989453123 chr21 48129895 49882882 1.0364219992584651 17.732864616842768 chr22 51304566 88144420 1.718061897258813 21.70546268482094 chrMT 16571 134899 8.14066743105425 15.161678791861583 chrX 155270560 118042826 0.7602395843745267 12.988116554338704 chrY 59373566 1174490 0.01978136196165142 0.9267483912419955