BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618661.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 = 29,377,386 number of mapped reads = 27,568,285 (93.84%) number of supplementary alignments = 39,212 (0.13%) number of secondary alignments = 0 number of mapped bases = 2,701,830,464 bp number of sequenced bases = 2,699,971,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,534,076 duplication rate = 24.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9404 >>>>>>> ACTG content number of A's = 740,795,145 bp (27.44%) number of C's = 591,568,177 bp (21.91%) number of T's = 753,157,237 bp (27.9%) number of G's = 587,503,050 bp (21.76%) number of N's = 26,947,797 bp (1%) GC percentage = 43.67% >>>>>>> Mismatches and indels general error rate = 0.0198 number of mismatches = 52,771,198 number of insertions = 492,032 mapped reads with insertion percentage = 1.76% number of deletions = 1,365,552 mapped reads with deletion percentage = 4.83% homopolymer indels = 53.48% >>>>>>> Coverage mean coverageData = 0.8728X std coverageData = 3.8621X There is a 18.24% of reference with a coverageData >= 1X There is a 12.15% of reference with a coverageData >= 2X There is a 8.92% of reference with a coverageData >= 3X There is a 6.87% of reference with a coverageData >= 4X There is a 5.45% of reference with a coverageData >= 5X There is a 4.43% of reference with a coverageData >= 6X There is a 3.66% of reference with a coverageData >= 7X There is a 3.07% of reference with a coverageData >= 8X There is a 2.6% of reference with a coverageData >= 9X There is a 2.23% of reference with a coverageData >= 10X There is a 1.92% of reference with a coverageData >= 11X There is a 1.67% of reference with a coverageData >= 12X There is a 1.46% of reference with a coverageData >= 13X There is a 1.29% of reference with a coverageData >= 14X There is a 1.14% of reference with a coverageData >= 15X There is a 1.01% of reference with a coverageData >= 16X There is a 0.9% of reference with a coverageData >= 17X There is a 0.81% of reference with a coverageData >= 18X There is a 0.73% of reference with a coverageData >= 19X There is a 0.65% of reference with a coverageData >= 20X There is a 0.59% of reference with a coverageData >= 21X There is a 0.54% of reference with a coverageData >= 22X There is a 0.49% of reference with a coverageData >= 23X There is a 0.44% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.37% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.31% of reference with a coverageData >= 28X There is a 0.28% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 222937164 0.8944297234067874 4.4760715591965194 chr2 243199373 196166495 0.8066077333184573 3.9413231713097736 chr3 198022430 187403594 0.946375589876359 4.26791832279117 chr4 191154276 152691230 0.7987853224899871 3.466321175159025 chr5 180915260 195730441 1.0818901678056345 3.62906229758908 chr6 171115067 139550802 0.8155377807846693 3.355464392134847 chr7 159138663 155228872 0.975431545506952 3.6356993493653316 chr8 146364022 106838653 0.7299516065498665 3.1617959445848505 chr9 141213431 113777844 0.8057154563435258 3.521145581223179 chr10 135534747 83719201 0.617695482915536 2.954398941166794 chr11 135006516 160270173 1.1871291678988294 4.715991971524611 chr12 133851895 119497515 0.8927592321348906 3.5488589302923943 chr13 115169878 49964283 0.43383117068162563 2.2478554435267997 chr14 107349540 82293330 0.7665922928034904 3.2953480884588053 chr15 102531392 113007444 1.1021740931791895 3.993668080732647 chr16 90354753 86447176 0.9567529446956708 5.869952510680033 chr17 81195210 93021072 1.145647286336226 4.413426187004633 chr18 78077248 60862891 0.7795214682771606 3.4722483028260567 chr19 59128983 70771236 1.1968958776104774 4.700441491397038 chr20 63025520 86753219 1.376477639533954 4.601755229519646 chr21 48129895 39720628 0.8252797559604067 5.265681940585768 chr22 51304566 55372061 1.0792813450561105 4.3694277113731195 chrMT 16571 5920 0.35725061855047974 1.0959059942395069 chrX 155270560 125985914 0.8113960173776664 3.340758325199923 chrY 59373566 3813306 0.06422565220354122 1.6189669923828054