BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,984,800 number of mapped reads = 28,354,068 (97.82%) number of supplementary alignments = 519,020 (1.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,227,667 number of mapped paired reads (second in pair) = 14,126,401 number of mapped paired reads (both in pair) = 28,053,616 number of mapped paired reads (singletons) = 300,452 number of mapped bases = 2,695,043,492 bp number of sequenced bases = 2,693,005,616 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,054,009 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 185,072.0453 std insert size = 4,216,335.6643 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.36 >>>>>>> ACTG content number of A's = 776,565,609 bp (28.84%) number of C's = 538,918,867 bp (20.01%) number of T's = 782,403,719 bp (29.05%) number of G's = 594,927,186 bp (22.09%) number of N's = 190,235 bp (0.01%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 25,557,301 number of insertions = 451,240 mapped reads with insertion percentage = 1.56% number of deletions = 1,418,114 mapped reads with deletion percentage = 4.87% homopolymer indels = 52.66% >>>>>>> Coverage mean coverageData = 0.8706X std coverageData = 3.5599X There is a 31.99% of reference with a coverageData >= 1X There is a 18.57% of reference with a coverageData >= 2X There is a 11.21% of reference with a coverageData >= 3X There is a 7.2% of reference with a coverageData >= 4X There is a 4.78% of reference with a coverageData >= 5X There is a 3.26% of reference with a coverageData >= 6X There is a 2.28% of reference with a coverageData >= 7X There is a 1.62% of reference with a coverageData >= 8X There is a 1.17% of reference with a coverageData >= 9X There is a 0.85% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 230021048 0.9228504509924571 4.9223780081155555 chr2 243199373 253682368 1.0431045313591332 6.53707830061816 chr3 198022430 186085366 0.9397186268242441 1.968885382460883 chr4 191154276 180697256 0.9452953906194597 3.027328303346272 chr5 180915260 153687774 0.8495014406192158 1.854681275122888 chr6 171115067 168859270 0.9868170755530253 2.0670047317893534 chr7 159138663 119790718 0.752744278114238 2.6753426641374696 chr8 146364022 136913154 0.9354290223044021 2.1925205917674075 chr9 141213431 105121899 0.7444185602996928 4.02457740704641 chr10 135534747 141436556 1.0435446195948557 4.405925375066751 chr11 135006516 126536114 0.9372593097654635 3.0496538975717393 chr12 133851895 121203659 0.9055057382639222 2.06853302759419 chr13 115169878 83170078 0.7221513076535515 1.7438421603985965 chr14 107349540 67619844 0.6299034350775979 1.6814459797181205 chr15 102531392 76096169 0.7421743479304368 1.81621080639096 chr16 90354753 78667790 0.8706546959405667 5.297685204102049 chr17 81195210 60187403 0.7412679023799557 3.2658643758535706 chr18 78077248 71843237 0.9201558564154311 4.334636110301014 chr19 59128983 41052019 0.6942791321136033 2.8813770248958 chr20 63025520 64658075 1.025903078625928 2.3093192757063226 chr21 48129895 38273485 0.7952123103530561 2.4620022913708404 chr22 51304566 35928700 0.7003021914267825 1.8545029149466141 chrMT 16571 4533720 273.5936274213988 186.46315089722657 chrX 155270560 144457691 0.9303611128857912 2.233499246800702 chrY 59373566 4520099 0.07612982181329651 2.963288531683061