BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472445.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 = 16,533,574 number of mapped reads = 16,305,457 (98.62%) number of supplementary alignments = 62,388 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,179,569 number of mapped paired reads (second in pair) = 8,125,888 number of mapped paired reads (both in pair) = 16,214,692 number of mapped paired reads (singletons) = 90,765 number of mapped bases = 1,593,872,447 bp number of sequenced bases = 1,593,685,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,489,706 duplication rate = 48.23% >>>>>>> Insert size mean insert size = 17,775.3002 std insert size = 1,262,102.7281 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 54.8344 >>>>>>> ACTG content number of A's = 435,472,824 bp (27.32%) number of C's = 362,224,956 bp (22.73%) number of T's = 436,213,894 bp (27.37%) number of G's = 359,578,380 bp (22.56%) number of N's = 195,223 bp (0.01%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 8,512,672 number of insertions = 90,907 mapped reads with insertion percentage = 0.55% number of deletions = 81,277 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.5149X std coverageData = 18.7116X There is a 4.09% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 145172523 0.5824359530883576 23.676228795125386 chr2 243199373 137852718 0.5668300715561466 20.91093415146936 chr3 198022430 110073838 0.555865504730954 23.663645753069225 chr4 191154276 43752663 0.22888665592811536 8.589322779883961 chr5 180915260 63211651 0.34939922149187413 11.669970475253823 chr6 171115067 150201533 0.8777808736152966 25.5533838010985 chr7 159138663 107276370 0.674106266683917 19.111000257266802 chr8 146364022 132524964 0.9054476789384758 24.54385142158579 chr9 141213431 58291048 0.4127868545308555 15.416554571530419 chr10 135534747 25781173 0.1902181807296988 7.778642386657047 chr11 135006516 51816735 0.38380914147877127 13.987299572938637 chr12 133851895 90104331 0.6731644030889514 19.978692147237734 chr13 115169878 78826031 0.6844327038359804 31.726110258738945 chr14 107349540 28087388 0.2616442324764503 8.492669748111423 chr15 102531392 31068512 0.3030146318505068 11.847493248823898 chr16 90354753 72289286 0.8000606896684229 20.57716240459227 chr17 81195210 54729170 0.6740443186242144 14.066240530791733 chr18 78077248 7137997 0.09142224121423952 2.8758090625448127 chr19 59128983 30211569 0.5109434911133175 11.930149652889911 chr20 63025520 70523053 1.1189602719660225 29.370448742802306 chr21 48129895 9308512 0.1934039540289876 10.068961164348371 chr22 51304566 11579943 0.22570979354936946 7.287322260883904 chrMT 16571 5284 0.31887031561161067 0.7465281519912977 chrX 155270560 83762942 0.5394644161777996 17.01476451723056 chrY 59373566 283213 0.004770018361369772 0.4009711562988124