BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082981.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,358,457 number of mapped reads = 2,723,624 (81.1%) number of supplementary alignments = 18,925 (0.56%) number of secondary alignments = 0 number of mapped bases = 183,748,676 bp number of sequenced bases = 183,671,757 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,964 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7148 >>>>>>> ACTG content number of A's = 51,624,807 bp (28.11%) number of C's = 33,862,290 bp (18.44%) number of T's = 58,205,944 bp (31.69%) number of G's = 39,960,588 bp (21.76%) number of N's = 18,128 bp (0.01%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,777,944 number of insertions = 16,961 mapped reads with insertion percentage = 0.62% number of deletions = 44,221 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.0594X std coverageData = 0.5667X There is a 4.93% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 21760257 0.08730271929793908 0.9460815534842476 chr2 243199373 18722080 0.0769824353124463 0.8466381059613496 chr3 198022430 8815102 0.04451567431022839 0.24841751694078604 chr4 191154276 9988203 0.05225205111289271 0.2780374929240838 chr5 180915260 11515020 0.06364869386916283 0.29482687367678384 chr6 171115067 12154604 0.07103175782878313 0.44435450736940424 chr7 159138663 9377063 0.0589238518360557 0.6363309556841531 chr8 146364022 11784524 0.08051516922649202 0.6945091824061324 chr9 141213431 5637503 0.03992186125695083 0.611531213301818 chr10 135534747 7219310 0.05326538145970789 0.4787446234589285 chr11 135006516 9043416 0.06698503352238198 0.5593391719902904 chr12 133851895 6007608 0.04488250241059344 0.26171119791154507 chr13 115169878 3878024 0.03367220724154974 0.2082404442045965 chr14 107349540 2396699 0.022326122682966316 0.2788204802879985 chr15 102531392 3589851 0.03501221362526708 0.2170717127702571 chr16 90354753 7579224 0.08388295854231376 0.41300095001132664 chr17 81195210 5441514 0.06701767259423308 0.4244392191171486 chr18 78077248 6935040 0.08882280277091734 1.3124000736228687 chr19 59128983 2815874 0.04762256776850026 0.7181781169523842 chr20 63025520 3710357 0.058870708246437316 0.30095492914917654 chr21 48129895 3592865 0.07464934216041817 0.3416476616653574 chr22 51304566 2672121 0.052083492919519095 0.2632089187540239 chrMT 16571 17951 1.0832780158107538 1.39101433737429 chrX 155270560 8724838 0.056191192973091615 0.35787631743043385 chrY 59373566 369628 0.0062254640389967485 0.128697866050789