BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504597.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 371,625,352 number of mapped reads = 355,400,145 (95.63%) number of supplementary alignments = 1,037,034 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 177,956,024 number of mapped paired reads (second in pair) = 177,444,121 number of mapped paired reads (both in pair) = 352,595,840 number of mapped paired reads (singletons) = 2,804,305 number of mapped bases = 34,151,382,308 bp number of sequenced bases = 34,140,395,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,842,762 duplication rate = 18.21% >>>>>>> Insert size mean insert size = 34,565.1338 std insert size = 1,768,037.3889 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.3703 >>>>>>> ACTG content number of A's = 9,702,218,681 bp (28.42%) number of C's = 7,322,552,361 bp (21.45%) number of T's = 9,604,634,821 bp (28.13%) number of G's = 7,502,415,894 bp (21.98%) number of N's = 8,574,031 bp (0.03%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 188,306,077 number of insertions = 3,453,615 mapped reads with insertion percentage = 0.94% number of deletions = 4,247,783 mapped reads with deletion percentage = 1.16% homopolymer indels = 40.41% >>>>>>> Coverage mean coverageData = 11.0319X std coverageData = 97.2833X There is a 90.92% of reference with a coverageData >= 1X There is a 89.25% of reference with a coverageData >= 2X There is a 86.4% of reference with a coverageData >= 3X There is a 82.4% of reference with a coverageData >= 4X There is a 77.37% of reference with a coverageData >= 5X There is a 71.59% of reference with a coverageData >= 6X There is a 65.33% of reference with a coverageData >= 7X There is a 58.88% of reference with a coverageData >= 8X There is a 52.48% of reference with a coverageData >= 9X There is a 46.33% of reference with a coverageData >= 10X There is a 40.56% of reference with a coverageData >= 11X There is a 35.26% of reference with a coverageData >= 12X There is a 30.48% of reference with a coverageData >= 13X There is a 26.22% of reference with a coverageData >= 14X There is a 22.49% of reference with a coverageData >= 15X There is a 19.25% of reference with a coverageData >= 16X There is a 16.46% of reference with a coverageData >= 17X There is a 14.08% of reference with a coverageData >= 18X There is a 12.05% of reference with a coverageData >= 19X There is a 10.34% of reference with a coverageData >= 20X There is a 8.9% of reference with a coverageData >= 21X There is a 7.69% of reference with a coverageData >= 22X There is a 6.67% of reference with a coverageData >= 23X There is a 5.82% of reference with a coverageData >= 24X There is a 5.11% of reference with a coverageData >= 25X There is a 4.51% of reference with a coverageData >= 26X There is a 4% of reference with a coverageData >= 27X There is a 3.57% of reference with a coverageData >= 28X There is a 3.21% of reference with a coverageData >= 29X There is a 2.9% of reference with a coverageData >= 30X There is a 2.64% of reference with a coverageData >= 31X There is a 2.41% of reference with a coverageData >= 32X There is a 2.21% of reference with a coverageData >= 33X There is a 2.04% of reference with a coverageData >= 34X There is a 1.9% of reference with a coverageData >= 35X There is a 1.77% of reference with a coverageData >= 36X There is a 1.65% of reference with a coverageData >= 37X There is a 1.55% of reference with a coverageData >= 38X There is a 1.46% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.3% of reference with a coverageData >= 41X There is a 1.24% of reference with a coverageData >= 42X There is a 1.17% of reference with a coverageData >= 43X There is a 1.12% of reference with a coverageData >= 44X There is a 1.07% of reference with a coverageData >= 45X There is a 1.02% of reference with a coverageData >= 46X There is a 0.97% of reference with a coverageData >= 47X There is a 0.93% of reference with a coverageData >= 48X There is a 0.9% of reference with a coverageData >= 49X There is a 0.86% of reference with a coverageData >= 50X There is a 0.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3176689562 12.744961473937511 176.23620861953538 chr2 243199373 2411940633 9.917544618834194 58.40425362882131 chr3 198022430 2019954485 10.20063477152563 16.76920854554866 chr4 191154276 1936221389 10.129103201437147 116.936329605575 chr5 180915260 1612187767 8.911286792501638 10.478718860741386 chr6 171115067 1600627718 9.354101576572448 23.073156205282167 chr7 159138663 2879949705 18.097108840231993 139.56217803874227 chr8 146364022 3002614859 20.514705854420974 68.63423349153132 chr9 141213431 1231210884 8.718794489172918 61.91404264054235 chr10 135534747 1663057221 12.270338476376098 264.1144960360664 chr11 135006516 1466698735 10.863910709317171 39.574966031357015 chr12 133851895 1277102784 9.54116326855141 9.008091357376893 chr13 115169878 828663299 7.195139157827362 6.596144812143246 chr14 107349540 1107773243 10.319310571801239 9.728413476766923 chr15 102531392 891281608 8.692768045127096 7.424724402752733 chr16 90354753 948387479 10.496265525732774 74.76151857951086 chr17 81195210 1058868537 13.041022210546657 45.85012365712377 chr18 78077248 582430308 7.459667482132567 96.30345352623574 chr19 59128983 682804323 11.547709572478187 91.47805803637704 chr20 63025520 1436664907 22.79497110059544 29.66891406899785 chr21 48129895 409611586 8.510543935323359 40.95953295646099 chr22 51304566 460535079 8.976493027930497 9.641695353679562 chrMT 16571 122353432 7383.587713475348 1565.2143605300435 chrX 155270560 1212621911 7.809734897587798 19.105248313331206 chrY 59373566 131130854 2.2085729868406423 118.98924827055576