BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472563.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 = 7,824,126 number of mapped reads = 7,675,216 (98.1%) number of supplementary alignments = 32,663 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,849,318 number of mapped paired reads (second in pair) = 3,825,898 number of mapped paired reads (both in pair) = 7,607,970 number of mapped paired reads (singletons) = 67,246 number of mapped bases = 751,473,709 bp number of sequenced bases = 751,405,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,312,076 duplication rate = 33.64% >>>>>>> Insert size mean insert size = 35,420.5352 std insert size = 1,882,795.5116 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 50.097 >>>>>>> ACTG content number of A's = 212,213,996 bp (28.24%) number of C's = 164,767,419 bp (21.93%) number of T's = 208,084,775 bp (27.69%) number of G's = 166,224,091 bp (22.12%) number of N's = 115,679 bp (0.02%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 4,582,061 number of insertions = 45,867 mapped reads with insertion percentage = 0.59% number of deletions = 30,687 mapped reads with deletion percentage = 0.4% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.2427X std coverageData = 55.0653X There is a 1.25% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 222864686 0.8941389397782082 161.21533703500555 chr2 243199373 15183669 0.06243301046668406 10.43919515328312 chr3 198022430 66193957 0.33427504651872014 34.12815478831768 chr4 191154276 33621392 0.17588616223264605 27.727272807309593 chr5 180915260 23572933 0.13029820148947083 12.729966778762044 chr6 171115067 65708041 0.3839991542065667 36.88520836705513 chr7 159138663 5963176 0.037471572825768934 6.099900973471441 chr8 146364022 13014500 0.08891870981790867 9.09356597024198 chr9 141213431 53315544 0.3775529255428968 58.19313150444775 chr10 135534747 13044893 0.09624759177069184 8.495896991853366 chr11 135006516 4423337 0.03276387785608807 2.5646263850577475 chr12 133851895 19182267 0.14330964085342235 14.823940787446992 chr13 115169878 147705618 1.282502166061164 109.6928586940305 chr14 107349540 2364044 0.02202192948381521 1.3473280161961503 chr15 102531392 872159 0.008506263135489276 0.3711286981917056 chr16 90354753 1717391 0.019007201535928053 0.4404923594783368 chr17 81195210 3707483 0.045661351205323567 5.0096842599778935 chr18 78077248 7087809 0.09077944191885452 25.33819920205298 chr19 59128983 1929856 0.032638071924896796 2.394709765481694 chr20 63025520 4637463 0.07358071777908377 2.3490298331157575 chr21 48129895 7394058 0.15362713756180021 18.7246838078984 chr22 51304566 6769990 0.1319568710512043 5.461011325798244 chrMT 16571 860 0.051897893911049424 0.2481567565363377 chrX 155270560 29483266 0.1898831690952876 39.99027933332909 chrY 59373566 1715317 0.028890247218770725 1.716288223540528