BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975191.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 = 4,385,628 number of mapped reads = 4,345,310 (99.08%) number of supplementary alignments = 61,179 (1.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,181,715 number of mapped paired reads (second in pair) = 2,163,595 number of mapped paired reads (both in pair) = 4,323,892 number of mapped paired reads (singletons) = 21,418 number of mapped bases = 618,930,716 bp number of sequenced bases = 618,476,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 534,730 duplication rate = 10.31% >>>>>>> Insert size mean insert size = 128,148.7572 std insert size = 3,509,750.2907 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.7063 >>>>>>> ACTG content number of A's = 182,641,087 bp (29.53%) number of C's = 125,226,430 bp (20.25%) number of T's = 181,085,778 bp (29.28%) number of G's = 129,466,259 bp (20.93%) number of N's = 57,078 bp (0.01%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 5,518,923 number of insertions = 108,347 mapped reads with insertion percentage = 2.35% number of deletions = 231,609 mapped reads with deletion percentage = 5.12% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.1999X std coverageData = 2.6588X There is a 10.64% of reference with a coverageData >= 1X There is a 6.11% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 66740955 0.26776645423082013 3.3828974766437954 chr2 243199373 44400756 0.1825693687129695 2.2870443911667886 chr3 198022430 48253633 0.24367761268256327 0.7974109941776135 chr4 191154276 32942119 0.17233262937837707 1.4871466704729326 chr5 180915260 54149705 0.29930977077334436 0.8119076134968745 chr6 171115067 31622745 0.18480397754804373 1.1053012932661657 chr7 159138663 27414500 0.17226800504161582 1.074808936484643 chr8 146364022 40856770 0.27914489805424997 1.153861027045489 chr9 141213431 22753983 0.16113186145870217 2.719636879450076 chr10 135534747 31512476 0.23250477606307113 9.582696955572331 chr11 135006516 24874047 0.1842433071897063 1.628556697497066 chr12 133851895 22308237 0.1666635873926178 0.5790805639024171 chr13 115169878 11637805 0.10104903471374695 0.44632435613400506 chr14 107349540 18540365 0.17271024170201382 0.6242233600814895 chr15 102531392 15871650 0.1547979569027991 0.5590685806053188 chr16 90354753 18269796 0.20220071876019627 3.4375533109523873 chr17 81195210 10868002 0.13385028501065518 1.5735913530658079 chr18 78077248 14729046 0.18864709473366684 2.474017608588433 chr19 59128983 9358271 0.15826876305313758 1.7085775990544871 chr20 63025520 11036069 0.1751047670848253 0.7712818365931569 chr21 48129895 6459158 0.13420261980625556 0.9066321353556309 chr22 51304566 5653753 0.11019980170965679 0.4917042751583259 chrMT 16571 79541 4.800012069277654 3.769373069235106 chrX 155270560 46652172 0.30045729209709815 1.1391685979314436 chrY 59373566 1945162 0.03276141439778099 2.2159854010976194