BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618589.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 = 57,387,688 number of mapped reads = 55,207,699 (96.2%) number of supplementary alignments = 185,727 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,924,806 number of mapped paired reads (second in pair) = 27,282,893 number of mapped paired reads (both in pair) = 54,039,940 number of mapped paired reads (singletons) = 1,167,759 number of mapped bases = 5,174,121,396 bp number of sequenced bases = 5,170,616,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,738,353 duplication rate = 16.73% >>>>>>> Insert size mean insert size = 67,395.4754 std insert size = 2,606,494.7049 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.5631 >>>>>>> ACTG content number of A's = 1,402,829,360 bp (27.13%) number of C's = 1,130,985,799 bp (21.87%) number of T's = 1,424,538,552 bp (27.55%) number of G's = 1,211,798,381 bp (23.44%) number of N's = 464,483 bp (0.01%) GC percentage = 45.31% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 66,776,533 number of insertions = 934,971 mapped reads with insertion percentage = 1.67% number of deletions = 2,576,464 mapped reads with deletion percentage = 4.55% homopolymer indels = 52.68% >>>>>>> Coverage mean coverageData = 1.6714X std coverageData = 6.3534X There is a 28.81% of reference with a coverageData >= 1X There is a 20.14% of reference with a coverageData >= 2X There is a 15.23% of reference with a coverageData >= 3X There is a 12.15% of reference with a coverageData >= 4X There is a 9.97% of reference with a coverageData >= 5X There is a 8.35% of reference with a coverageData >= 6X There is a 7.1% of reference with a coverageData >= 7X There is a 6.11% of reference with a coverageData >= 8X There is a 5.31% of reference with a coverageData >= 9X There is a 4.65% of reference with a coverageData >= 10X There is a 4.1% of reference with a coverageData >= 11X There is a 3.63% of reference with a coverageData >= 12X There is a 3.24% of reference with a coverageData >= 13X There is a 2.9% of reference with a coverageData >= 14X There is a 2.61% of reference with a coverageData >= 15X There is a 2.35% of reference with a coverageData >= 16X There is a 2.13% of reference with a coverageData >= 17X There is a 1.93% of reference with a coverageData >= 18X There is a 1.76% of reference with a coverageData >= 19X There is a 1.61% of reference with a coverageData >= 20X There is a 1.47% of reference with a coverageData >= 21X There is a 1.35% of reference with a coverageData >= 22X There is a 1.24% of reference with a coverageData >= 23X There is a 1.14% of reference with a coverageData >= 24X There is a 1.05% of reference with a coverageData >= 25X There is a 0.97% of reference with a coverageData >= 26X There is a 0.9% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.71% of reference with a coverageData >= 30X There is a 0.66% of reference with a coverageData >= 31X There is a 0.62% of reference with a coverageData >= 32X There is a 0.58% of reference with a coverageData >= 33X There is a 0.54% of reference with a coverageData >= 34X There is a 0.5% of reference with a coverageData >= 35X There is a 0.47% of reference with a coverageData >= 36X There is a 0.44% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.38% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.3% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 459611767 1.8439744107999634 7.808893605954498 chr2 243199373 438165239 1.8016709237157449 6.909117570692547 chr3 198022430 321861510 1.6253790542818811 5.047869038176108 chr4 191154276 266088045 1.3920067631654758 5.339978226877799 chr5 180915260 292989289 1.6194835582139395 5.240783458552757 chr6 171115067 279983035 1.6362266626117734 5.48239346083682 chr7 159138663 257101325 1.615580526776199 5.357953394497642 chr8 146364022 252672980 1.726332581923719 5.455663130571866 chr9 141213431 227123668 1.6083715719647091 7.489267088157846 chr10 135534747 259396514 1.9138746317208235 6.297075865195532 chr11 135006516 255814200 1.8948285429423273 6.821916560997621 chr12 133851895 233614578 1.7453214091589813 6.968969089284964 chr13 115169878 139804350 1.21389683160036 4.336766615970076 chr14 107349540 162698910 1.515599507925232 5.3692490500149805 chr15 102531392 165247685 1.611678938290431 5.631903742987134 chr16 90354753 179220991 1.9835258804813511 10.088310652009124 chr17 81195210 171095545 2.1072122973756704 7.019516539964301 chr18 78077248 130680155 1.673729010018386 7.213123505570779 chr19 59128983 110826391 1.8743158663831576 7.064236808806661 chr20 63025520 141992727 2.252940189942106 6.766417514423102 chr21 48129895 65474746 1.360375832941252 8.686856153559889 chr22 51304566 92139690 1.795935472877794 6.6546493529179855 chrMT 16571 4651 0.28067105183754754 0.854270768347179 chrX 155270560 263689302 1.6982569136093797 5.205597617809211 chrY 59373566 6824103 0.11493503691524945 3.0417233393811807