BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926939.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 6,091,826 number of mapped reads = 6,009,836 (98.65%) number of supplementary alignments = 43,609 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,015,004 number of mapped paired reads (second in pair) = 2,994,832 number of mapped paired reads (both in pair) = 5,962,886 number of mapped paired reads (singletons) = 46,950 number of mapped bases = 568,018,004 bp number of sequenced bases = 567,591,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,451 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 72,517.5804 std insert size = 2,617,361.8021 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.7191 >>>>>>> ACTG content number of A's = 163,039,680 bp (28.72%) number of C's = 113,054,828 bp (19.92%) number of T's = 164,665,721 bp (29.01%) number of G's = 126,706,535 bp (22.32%) number of N's = 124,290 bp (0.02%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 5,102,085 number of insertions = 89,952 mapped reads with insertion percentage = 1.47% number of deletions = 303,822 mapped reads with deletion percentage = 4.92% homopolymer indels = 53.37% >>>>>>> Coverage mean coverageData = 0.1835X std coverageData = 0.7967X There is a 12.09% of reference with a coverageData >= 1X There is a 3.98% of reference with a coverageData >= 2X There is a 1.27% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.08% 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 0.01% 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% 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 46071242 0.1848390259376726 1.0158330975353245 chr2 243199373 51508566 0.21179563649615166 1.2973423334445124 chr3 198022430 40153122 0.20277057503031348 0.6076221733330899 chr4 191154276 34159400 0.17870068467628733 0.6809691550037159 chr5 180915260 32940168 0.18207512180011792 0.5753683884572719 chr6 171115067 32458943 0.18969073600047154 0.6595736070925401 chr7 159138663 30572770 0.19211403076824896 0.653516487463337 chr8 146364022 29031352 0.19835032956391427 0.633552359469661 chr9 141213431 22270647 0.15770912754042496 0.9175558946418861 chr10 135534747 28215644 0.20818015029016876 0.9848532941353428 chr11 135006516 27636559 0.20470537140592532 0.727793086389068 chr12 133851895 24845923 0.18562249716374954 0.5865682498112634 chr13 115169878 15706405 0.1363759801846799 0.4931521282037939 chr14 107349540 18573866 0.17302231569879106 0.5714548168154386 chr15 102531392 14762170 0.14397707582083738 0.518733391336298 chr16 90354753 20016857 0.22153629261761137 1.2460632490629673 chr17 81195210 14393827 0.17727433674966786 0.6434793565336805 chr18 78077248 16191005 0.20737161483970337 0.9906222890679388 chr19 59128983 8140814 0.13767891120332645 0.6687028142700744 chr20 63025520 13154681 0.2087199121879518 0.6476092996724998 chr21 48129895 7641638 0.15877113382441413 0.6465004138089276 chr22 51304566 7595570 0.1480486161796983 0.5436765850771235 chrMT 16571 36665 2.2126003258704965 2.451075668130273 chrX 155270560 31086937 0.2002114051755851 0.6283388009626687 chrY 59373566 853233 0.014370587072368199 0.4772173662699967