BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472694.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 = 11,844,280 number of mapped reads = 11,731,707 (99.05%) number of supplementary alignments = 68,277 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,883,243 number of mapped paired reads (second in pair) = 5,848,464 number of mapped paired reads (both in pair) = 11,661,996 number of mapped paired reads (singletons) = 69,711 number of mapped bases = 1,143,887,918 bp number of sequenced bases = 1,143,777,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,364,835 duplication rate = 48.47% >>>>>>> Insert size mean insert size = 15,893.9849 std insert size = 1,253,740.3551 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 54.5985 >>>>>>> ACTG content number of A's = 301,002,470 bp (26.32%) number of C's = 271,945,309 bp (23.78%) number of T's = 301,466,371 bp (26.36%) number of G's = 269,169,832 bp (23.53%) number of N's = 193,815 bp (0.02%) GC percentage = 47.31% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 7,210,166 number of insertions = 69,209 mapped reads with insertion percentage = 0.58% number of deletions = 51,569 mapped reads with deletion percentage = 0.43% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.3695X std coverageData = 22.9553X There is a 2.27% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.13% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 119638742 0.4799937569664069 30.007846628125648 chr2 243199373 97467610 0.4007724559388564 25.63354364128436 chr3 198022430 99408240 0.5020049496413108 21.706230442244777 chr4 191154276 30303071 0.15852677551403557 17.747925093406888 chr5 180915260 67117682 0.3709896113793828 25.501699720908274 chr6 171115067 60123352 0.3513621158796028 16.78942480875906 chr7 159138663 51816262 0.3256044824254933 17.141943591943047 chr8 146364022 47638595 0.325480226281292 18.446394755129873 chr9 141213431 62612042 0.44338588444890914 23.99546954372728 chr10 135534747 44973397 0.3318218980406552 30.777985563042954 chr11 135006516 43182455 0.3198545987217387 13.496758340864941 chr12 133851895 56117464 0.4192504260025605 24.673978966903565 chr13 115169878 24874383 0.21597993704569177 16.53169681027899 chr14 107349540 43619761 0.4063339349195162 20.720715421868764 chr15 102531392 18028056 0.17582962299000096 12.103186971726984 chr16 90354753 61882547 0.6848842473179025 36.062800414638865 chr17 81195210 68860893 0.8480905831760273 35.40532499310204 chr18 78077248 12094297 0.15490168147319947 8.704949398810758 chr19 59128983 41307366 0.698597606524029 33.472130352571256 chr20 63025520 20704494 0.32850968940835396 22.580655629729595 chr21 48129895 12865380 0.26730538265250736 30.754344016134635 chr22 51304566 24188186 0.47146263745803835 22.40363660372934 chrMT 16571 1830 0.11043389053165167 0.4010957458968695 chrX 155270560 34386504 0.2214618405446596 13.364971093755255 chrY 59373566 675309 0.011373899960800737 0.511946317682509