BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472758.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 = 16,931,792 number of mapped reads = 16,778,105 (99.09%) number of supplementary alignments = 103,390 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,419,063 number of mapped paired reads (second in pair) = 8,359,042 number of mapped paired reads (both in pair) = 16,681,846 number of mapped paired reads (singletons) = 96,259 number of mapped bases = 1,653,527,445 bp number of sequenced bases = 1,653,293,454 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,622,527 duplication rate = 46.79% >>>>>>> Insert size mean insert size = 44,307.3621 std insert size = 2,040,879.0932 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 54.9921 >>>>>>> ACTG content number of A's = 461,452,864 bp (27.91%) number of C's = 367,080,240 bp (22.2%) number of T's = 458,967,054 bp (27.76%) number of G's = 365,474,352 bp (22.11%) number of N's = 318,944 bp (0.02%) GC percentage = 44.31% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,154,312 number of insertions = 94,014 mapped reads with insertion percentage = 0.56% number of deletions = 95,063 mapped reads with deletion percentage = 0.56% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.5341X std coverageData = 17.629X There is a 4.87% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187083542 0.7505840557163547 27.383146624911483 chr2 243199373 134963184 0.5549487333587821 19.442918407050257 chr3 198022430 185487033 0.9366970852746328 24.153029197396563 chr4 191154276 50763044 0.2655605988118205 9.424929292445517 chr5 180915260 84488112 0.4670037895089668 14.919553174617889 chr6 171115067 116734517 0.6821989380981863 18.77067027057409 chr7 159138663 75392775 0.47375523696589056 15.690559486874042 chr8 146364022 58725894 0.4012317589906077 12.341087609743626 chr9 141213431 95800156 0.6784068294466976 17.157800890219782 chr10 135534747 34420766 0.2539626683333094 8.01150300260075 chr11 135006516 83643313 0.6195501926736633 24.18542206245107 chr12 133851895 78382511 0.5855913433276384 16.864496335761036 chr13 115169878 40985424 0.3558693011726556 13.474359295080546 chr14 107349540 39426813 0.367275099641787 12.57544891093743 chr15 102531392 42039381 0.4100147299277864 13.464269502160628 chr16 90354753 61445686 0.680049294141726 17.675999941998754 chr17 81195210 68439255 0.8428976906396326 19.56083195242924 chr18 78077248 30147158 0.3861196286016638 13.094233134074758 chr19 59128983 51656752 0.8736282847956306 24.13518742344117 chr20 63025520 32505014 0.5157436860497144 13.375218049542479 chr21 48129895 10825396 0.224920415887049 11.481834098815739 chr22 51304566 12756980 0.248651942597078 7.995758697947038 chrMT 16571 1833 0.11061492969645767 0.3988580369291554 chrX 155270560 75681492 0.487416880572853 15.375285958825895 chrY 59373566 1731414 0.02916136113502093 1.0827708492581858