BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472700.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 = 12,580,182 number of mapped reads = 12,436,574 (98.86%) number of supplementary alignments = 39,400 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,239,072 number of mapped paired reads (second in pair) = 6,197,502 number of mapped paired reads (both in pair) = 12,367,674 number of mapped paired reads (singletons) = 68,900 number of mapped bases = 1,224,079,525 bp number of sequenced bases = 1,223,906,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,486,352 duplication rate = 46.75% >>>>>>> Insert size mean insert size = 21,543.4785 std insert size = 1,424,830.3606 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.0615 >>>>>>> ACTG content number of A's = 328,888,298 bp (26.87%) number of C's = 285,129,063 bp (23.3%) number of T's = 326,470,814 bp (26.67%) number of G's = 283,178,573 bp (23.14%) number of N's = 239,802 bp (0.02%) GC percentage = 46.43% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 7,421,141 number of insertions = 73,481 mapped reads with insertion percentage = 0.58% number of deletions = 64,726 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.3954X std coverageData = 13.3935X There is a 3.63% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 123327327 0.4947924563044519 13.801589773427663 chr2 243199373 82300846 0.3384089563421695 11.038691396824138 chr3 198022430 113760192 0.574481345370825 14.166002049194224 chr4 191154276 42344056 0.22151770227729564 8.759271914495992 chr5 180915260 61521188 0.34005527228604154 13.013993323507687 chr6 171115067 105775081 0.6181517668458734 18.210596191079745 chr7 159138663 57253536 0.3597713774936013 12.266556077937402 chr8 146364022 74872518 0.511550017394302 17.441933198179864 chr9 141213431 71782221 0.5083243179609452 16.052901099925567 chr10 135534747 38466227 0.28381081494917315 14.801480694381379 chr11 135006516 67790814 0.5021299416392613 19.12497159762481 chr12 133851895 69226146 0.517184653978937 14.951108623142149 chr13 115169878 25720804 0.22332926322974833 8.226256225942238 chr14 107349540 26237414 0.24441105197097257 9.819102054126162 chr15 102531392 36738921 0.3583187576347349 11.938210792930144 chr16 90354753 32992154 0.3651402157006616 9.81091789935129 chr17 81195210 39121274 0.4818175111561384 13.222903782776653 chr18 78077248 23677379 0.3032558089137568 12.89224241324318 chr19 59128983 32183323 0.5442901495532233 17.131233581906123 chr20 63025520 27232143 0.4320812109126589 13.79306839833991 chr21 48129895 6166262 0.12811708814241127 5.992573808244549 chr22 51304566 16402374 0.31970593026749317 10.912787912008925 chrMT 16571 4082 0.2463339569126788 0.8019030776857181 chrX 155270560 46210015 0.2976096370103901 10.301972314670591 chrY 59373566 2973228 0.050076628377012086 1.9105571374108454