BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630573.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 30,928,508 number of mapped reads = 30,379,221 (98.22%) number of supplementary alignments = 60,689 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,255,417 number of mapped paired reads (second in pair) = 15,123,804 number of mapped paired reads (both in pair) = 30,183,384 number of mapped paired reads (singletons) = 195,837 number of mapped bases = 2,936,980,421 bp number of sequenced bases = 2,934,777,416 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,935,042 duplication rate = 10.31% >>>>>>> Insert size mean insert size = 33,138.3745 std insert size = 1,821,344.0837 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.023 >>>>>>> ACTG content number of A's = 864,065,407 bp (29.44%) number of C's = 574,467,559 bp (19.57%) number of T's = 874,939,595 bp (29.81%) number of G's = 620,863,326 bp (21.16%) number of N's = 441,529 bp (0.02%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 26,471,090 number of insertions = 543,356 mapped reads with insertion percentage = 1.76% number of deletions = 1,645,150 mapped reads with deletion percentage = 5.27% homopolymer indels = 54.51% >>>>>>> Coverage mean coverageData = 0.9487X std coverageData = 4.69X There is a 16.52% of reference with a coverageData >= 1X There is a 11.42% of reference with a coverageData >= 2X There is a 8.61% of reference with a coverageData >= 3X There is a 6.86% of reference with a coverageData >= 4X There is a 5.65% of reference with a coverageData >= 5X There is a 4.74% of reference with a coverageData >= 6X There is a 4.05% of reference with a coverageData >= 7X There is a 3.49% of reference with a coverageData >= 8X There is a 3.04% of reference with a coverageData >= 9X There is a 2.67% of reference with a coverageData >= 10X There is a 2.36% of reference with a coverageData >= 11X There is a 2.09% of reference with a coverageData >= 12X There is a 1.87% of reference with a coverageData >= 13X There is a 1.68% of reference with a coverageData >= 14X There is a 1.51% of reference with a coverageData >= 15X There is a 1.36% of reference with a coverageData >= 16X There is a 1.23% of reference with a coverageData >= 17X There is a 1.12% of reference with a coverageData >= 18X There is a 1.02% of reference with a coverageData >= 19X There is a 0.93% of reference with a coverageData >= 20X There is a 0.85% of reference with a coverageData >= 21X There is a 0.78% of reference with a coverageData >= 22X There is a 0.71% of reference with a coverageData >= 23X There is a 0.66% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.56% of reference with a coverageData >= 26X There is a 0.51% of reference with a coverageData >= 27X There is a 0.47% of reference with a coverageData >= 28X There is a 0.44% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.35% of reference with a coverageData >= 32X There is a 0.32% of reference with a coverageData >= 33X There is a 0.3% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% 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 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 253774992 1.0181518945944772 5.99763890495985 chr2 243199373 264950279 1.0894365216969535 5.571246505348053 chr3 198022430 213015335 1.075713165422725 4.34751280955568 chr4 191154276 192422207 1.0066330245209896 4.342357177728057 chr5 180915260 190985641 1.0556635244589097 4.258593978597581 chr6 171115067 183135843 1.0702496642215615 4.507982915841134 chr7 159138663 159684817 1.0034319378440424 4.272820967918606 chr8 146364022 155818062 1.0645926496881863 4.275499741784542 chr9 141213431 132111793 0.9355469381662428 5.672077690590559 chr10 135534747 143273621 1.057098819094708 4.471402728934122 chr11 135006516 145696727 1.079182926252241 6.108414740774274 chr12 133851895 137278263 1.025598203148338 4.312951867886744 chr13 115169878 100010749 0.8683759220444777 3.843173029710195 chr14 107349540 96931233 0.9029496819455398 3.9582674363893107 chr15 102531392 95305688 0.929526910158403 4.076771692782937 chr16 90354753 86441641 0.956691686158447 5.124945371942733 chr17 81195210 75998058 0.9359918891767137 4.2520925720262746 chr18 78077248 84809075 1.0862200855235062 6.2180642555112575 chr19 59128983 44961062 0.7603895707118792 4.172655355618348 chr20 63025520 68448629 1.0860462396819575 4.526681587117208 chr21 48129895 44057863 0.9153949535938111 4.6211963381214805 chr22 51304566 31737988 0.6186191692957699 3.2185955439261487 chrMT 16571 4316 0.2604550117675457 1.126318916401105 chrX 155270560 5914444 0.03809121317009483 1.4045561282439543 chrY 59373566 30212095 0.5088475736828743 3.6819782175866593