BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124830.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 25,641,394 number of mapped reads = 25,077,867 (97.8%) number of supplementary alignments = 287,585 (1.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,577,537 number of mapped paired reads (second in pair) = 12,500,330 number of mapped paired reads (both in pair) = 24,891,110 number of mapped paired reads (singletons) = 186,757 number of mapped bases = 2,138,040,276 bp number of sequenced bases = 2,136,825,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,008,713 duplication rate = 12.76% >>>>>>> Insert size mean insert size = 116,385.3113 std insert size = 3,262,555.5812 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.314 >>>>>>> ACTG content number of A's = 615,262,081 bp (28.79%) number of C's = 388,150,844 bp (18.16%) number of T's = 650,516,837 bp (30.44%) number of G's = 482,876,067 bp (22.6%) number of N's = 19,823 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 16,987,612 number of insertions = 317,277 mapped reads with insertion percentage = 1.23% number of deletions = 690,412 mapped reads with deletion percentage = 2.7% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.6906X std coverageData = 8.4327X There is a 28.45% of reference with a coverageData >= 1X There is a 14.51% of reference with a coverageData >= 2X There is a 7.87% of reference with a coverageData >= 3X There is a 4.69% of reference with a coverageData >= 4X There is a 2.91% of reference with a coverageData >= 5X There is a 1.9% of reference with a coverageData >= 6X There is a 1.27% of reference with a coverageData >= 7X There is a 0.88% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% 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 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% 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 187689358 0.7530146053277035 9.59985647833534 chr2 243199373 184068194 0.7568613016119906 8.62599395917491 chr3 198022430 233641466 1.1798737446055985 2.423485059645988 chr4 191154276 137110992 0.7172792305205875 6.507000504366549 chr5 180915260 117515269 0.6495597386312244 1.6664490761098045 chr6 171115067 93303891 0.5452698738679744 4.389590230563256 chr7 159138663 146845241 0.9227502495732292 15.414732472073092 chr8 146364022 134448299 0.9185884424520665 3.2577533287984832 chr9 141213431 84637519 0.5993588456894019 10.415382840178744 chr10 135534747 109608435 0.808710957345868 22.602493000324 chr11 135006516 92808564 0.6874376641198563 5.906213990251204 chr12 133851895 100492514 0.7507739356248935 1.7480021635034844 chr13 115169878 48365365 0.41994804405367175 1.154651672894393 chr14 107349540 56128944 0.5228615232072722 2.6141924463198776 chr15 102531392 52670768 0.5137038225327127 1.520668542391214 chr16 90354753 52848289 0.5848977197690972 11.327948095699666 chr17 81195210 51467075 0.6338683648949243 5.9106600955752695 chr18 78077248 49560423 0.6347613968156255 10.502503809856623 chr19 59128983 23334451 0.3946364340479186 5.4001791466729925 chr20 63025520 39378087 0.6247959080702548 2.228707165512148 chr21 48129895 25627213 0.5324593581598298 3.576251881475717 chr22 51304566 15083640 0.2940019022868257 1.196442222863043 chrMT 16571 2068380 124.81926256713535 72.17064855106162 chrX 155270560 72245698 0.46528909279389474 2.9872758395067636 chrY 59373566 27092201 0.4563007214355291 11.774804460265539