BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104286.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 121,795,034 number of mapped reads = 119,570,410 (98.17%) number of supplementary alignments = 107,821 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 60,270,199 number of mapped paired reads (second in pair) = 59,300,211 number of mapped paired reads (both in pair) = 118,377,820 number of mapped paired reads (singletons) = 1,192,590 number of mapped bases = 10,334,252,958 bp number of sequenced bases = 10,331,619,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,660,444 duplication rate = 28.28% >>>>>>> Insert size mean insert size = 10,855.9327 std insert size = 967,832.3319 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.2637 >>>>>>> ACTG content number of A's = 3,227,714,564 bp (31.24%) number of C's = 1,936,616,554 bp (18.74%) number of T's = 3,260,683,973 bp (31.56%) number of G's = 1,901,161,970 bp (18.4%) number of N's = 5,442,535 bp (0.05%) GC percentage = 37.15% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 65,095,083 number of insertions = 1,023,551 mapped reads with insertion percentage = 0.85% number of deletions = 1,188,428 mapped reads with deletion percentage = 0.98% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 3.3383X std coverageData = 28.3538X There is a 67.14% of reference with a coverageData >= 1X There is a 53.6% of reference with a coverageData >= 2X There is a 42.28% of reference with a coverageData >= 3X There is a 33.83% of reference with a coverageData >= 4X There is a 26.71% of reference with a coverageData >= 5X There is a 21.18% of reference with a coverageData >= 6X There is a 16.64% of reference with a coverageData >= 7X There is a 13.09% of reference with a coverageData >= 8X There is a 10.24% of reference with a coverageData >= 9X There is a 8.03% of reference with a coverageData >= 10X There is a 6.28% of reference with a coverageData >= 11X There is a 4.92% of reference with a coverageData >= 12X There is a 3.85% of reference with a coverageData >= 13X There is a 3.03% of reference with a coverageData >= 14X There is a 2.39% of reference with a coverageData >= 15X There is a 1.89% of reference with a coverageData >= 16X There is a 1.51% of reference with a coverageData >= 17X There is a 1.21% of reference with a coverageData >= 18X There is a 0.97% of reference with a coverageData >= 19X There is a 0.79% of reference with a coverageData >= 20X There is a 0.64% of reference with a coverageData >= 21X There is a 0.53% of reference with a coverageData >= 22X There is a 0.44% of reference with a coverageData >= 23X There is a 0.37% of reference with a coverageData >= 24X There is a 0.31% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 734727028 2.947744021869458 46.10200322653491 chr2 243199373 1004843008 4.131766441684042 14.633364466510605 chr3 198022430 794962322 4.014506447577681 5.151947909432585 chr4 191154276 1014531276 5.307395142968185 12.511341753429063 chr5 180915260 804218983 4.445279978040547 4.932243802238417 chr6 171115067 681876235 3.984898857562321 11.79885245719056 chr7 159138663 597664818 3.7556229688821756 26.379035374500038 chr8 146364022 638319530 4.361177844648188 84.23055191510264 chr9 141213431 412687663 2.922439176483149 17.354935467625882 chr10 135534747 416491071 3.072946828904325 39.956455992395675 chr11 135006516 472699235 3.501306818405713 11.431829811433818 chr12 133851895 408461092 3.0515899083834412 4.449403867173858 chr13 115169878 406176738 3.526761902100825 4.6527138600875455 chr14 107349540 239597783 2.231940472218139 4.469651414876762 chr15 102531392 136906892 1.335268051369087 2.427781913679898 chr16 90354753 170930616 1.8917722679182134 15.674670897260103 chr17 81195210 84735502 1.0436022272742445 5.417310176249194 chr18 78077248 290389958 3.7192647722419725 18.290089827903365 chr19 59128983 39300617 0.6646591063472206 29.0528615040954 chr20 63025520 102594796 1.6278294252867727 4.204154814025227 chr21 48129895 100706241 2.0923843902007264 5.634010490528246 chr22 51304566 18191104 0.3545708582740959 1.448570463802016 chrMT 16571 67722346 4086.7989861806773 843.6227071172638 chrX 155270560 679589075 4.376805718997858 7.433046688734937 chrY 59373566 15929029 0.26828486266093565 9.463689972244916