BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124841.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 = 128,349,802 number of mapped reads = 124,524,057 (97.02%) number of supplementary alignments = 2,313,105 (1.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 63,792,344 number of mapped paired reads (second in pair) = 60,731,713 number of mapped paired reads (both in pair) = 121,315,110 number of mapped paired reads (singletons) = 3,208,947 number of mapped bases = 16,797,221,377 bp number of sequenced bases = 16,784,352,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,058,229 duplication rate = 21.14% >>>>>>> Insert size mean insert size = 105,022.7189 std insert size = 3,153,497.5045 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 53.5901 >>>>>>> ACTG content number of A's = 4,725,546,503 bp (28.15%) number of C's = 3,410,406,466 bp (20.32%) number of T's = 4,843,475,349 bp (28.86%) number of G's = 3,804,619,549 bp (22.67%) number of N's = 305,004 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 203,305,605 number of insertions = 2,937,229 mapped reads with insertion percentage = 2.2% number of deletions = 6,341,624 mapped reads with deletion percentage = 4.87% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 5.426X std coverageData = 47.0831X There is a 53.46% of reference with a coverageData >= 1X There is a 45.19% of reference with a coverageData >= 2X There is a 38.8% of reference with a coverageData >= 3X There is a 33.96% of reference with a coverageData >= 4X There is a 29.93% of reference with a coverageData >= 5X There is a 26.59% of reference with a coverageData >= 6X There is a 23.74% of reference with a coverageData >= 7X There is a 21.3% of reference with a coverageData >= 8X There is a 19.19% of reference with a coverageData >= 9X There is a 17.34% of reference with a coverageData >= 10X There is a 15.71% of reference with a coverageData >= 11X There is a 14.27% of reference with a coverageData >= 12X There is a 13% of reference with a coverageData >= 13X There is a 11.86% of reference with a coverageData >= 14X There is a 10.85% of reference with a coverageData >= 15X There is a 9.94% of reference with a coverageData >= 16X There is a 9.12% of reference with a coverageData >= 17X There is a 8.38% of reference with a coverageData >= 18X There is a 7.71% of reference with a coverageData >= 19X There is a 7.11% of reference with a coverageData >= 20X There is a 6.56% of reference with a coverageData >= 21X There is a 6.06% of reference with a coverageData >= 22X There is a 5.6% of reference with a coverageData >= 23X There is a 5.19% of reference with a coverageData >= 24X There is a 4.81% of reference with a coverageData >= 25X There is a 4.46% of reference with a coverageData >= 26X There is a 4.14% of reference with a coverageData >= 27X There is a 3.85% of reference with a coverageData >= 28X There is a 3.59% of reference with a coverageData >= 29X There is a 3.34% of reference with a coverageData >= 30X There is a 3.11% of reference with a coverageData >= 31X There is a 2.9% of reference with a coverageData >= 32X There is a 2.71% of reference with a coverageData >= 33X There is a 2.54% of reference with a coverageData >= 34X There is a 2.37% of reference with a coverageData >= 35X There is a 2.22% of reference with a coverageData >= 36X There is a 2.08% of reference with a coverageData >= 37X There is a 1.95% of reference with a coverageData >= 38X There is a 1.83% of reference with a coverageData >= 39X There is a 1.71% of reference with a coverageData >= 40X There is a 1.61% of reference with a coverageData >= 41X There is a 1.51% of reference with a coverageData >= 42X There is a 1.42% of reference with a coverageData >= 43X There is a 1.34% of reference with a coverageData >= 44X There is a 1.26% of reference with a coverageData >= 45X There is a 1.19% of reference with a coverageData >= 46X There is a 1.12% of reference with a coverageData >= 47X There is a 1.05% of reference with a coverageData >= 48X There is a 0.99% of reference with a coverageData >= 49X There is a 0.94% of reference with a coverageData >= 50X There is a 0.89% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1517076155 6.086549148457287 50.261782685750504 chr2 243199373 1403286711 5.770108260106411 67.14529181876044 chr3 198022430 1176997748 5.943759744792547 10.862812769906572 chr4 191154276 660823668 3.457017451181683 40.93880602825922 chr5 180915260 914959511 5.057392676549231 11.182208549919702 chr6 171115067 944107943 5.517386397072795 33.49266934003594 chr7 159138663 1425878884 8.959977777367653 72.73590420035654 chr8 146364022 1092168609 7.462001891421103 19.144662509074124 chr9 141213431 706129186 5.000439271247506 76.21316415693369 chr10 135534747 952419603 7.0271249556396045 101.5065249691665 chr11 135006516 599287187 4.438950094823571 27.72823690362765 chr12 133851895 868568225 6.489024492331618 20.08514426408504 chr13 115169878 359767463 3.1237982469687084 7.057752067955492 chr14 107349540 401544685 3.7405347521749976 9.940299026198048 chr15 102531392 371000140 3.6184053757896897 11.325635729822189 chr16 90354753 598361253 6.622355029845525 55.617679052251944 chr17 81195210 405225506 4.99075630200353 66.13537761085279 chr18 78077248 437730113 5.606372204614589 57.021220063894056 chr19 59128983 250081512 4.229423529912564 33.86012361225542 chr20 63025520 427392786 6.781265525456989 16.745333663107125 chr21 48129895 162951106 3.3856526385524006 22.287768329482137 chr22 51304566 160107606 3.1207282018524434 10.068722783801247 chrMT 16571 16769185 1011.9597489590248 428.14170004729823 chrX 155270560 803862518 5.177172787938679 15.822520682178638 chrY 59373566 140724074 2.3701469101586388 59.46940603045978