BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085033.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,195,751 number of mapped reads = 2,880,204 (90.13%) number of supplementary alignments = 20,875 (0.65%) number of secondary alignments = 0 number of mapped bases = 190,485,388 bp number of sequenced bases = 190,418,319 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,685 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9667 >>>>>>> ACTG content number of A's = 53,209,627 bp (27.94%) number of C's = 37,019,980 bp (19.44%) number of T's = 57,738,795 bp (30.32%) number of G's = 42,429,618 bp (22.28%) number of N's = 20,299 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,719,650 number of insertions = 13,782 mapped reads with insertion percentage = 0.47% number of deletions = 39,031 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.84% >>>>>>> Coverage mean coverageData = 0.0615X std coverageData = 0.4281X There is a 5.11% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17066905 0.06847286851895146 0.6317597905774847 chr2 243199373 18657664 0.07671756620852802 0.5584081331088021 chr3 198022430 11367725 0.057406249382961315 0.28273646025319166 chr4 191154276 11547436 0.06040898609037655 0.2909491617312369 chr5 180915260 9562911 0.05285850955856349 0.26705200698587234 chr6 171115067 10451913 0.061081196315693226 0.3875333131617342 chr7 159138663 17859353 0.112225103964836 0.5153620439490117 chr8 146364022 11252837 0.07688253469831541 0.7072652440806158 chr9 141213431 6572443 0.04654261958977542 0.3887625341649317 chr10 135534747 14123001 0.10420206856622531 0.5938008411644986 chr11 135006516 7395584 0.05477945968178306 0.39912630483534 chr12 133851895 7886865 0.058922326052985655 0.28909039323465946 chr13 115169878 3895258 0.03382184706317046 0.21120451302713175 chr14 107349540 6465092 0.06022468284447237 0.2967991758177989 chr15 102531392 3308644 0.032269570669634526 0.22179988093013167 chr16 90354753 5669729 0.06274964859900618 0.3106536693501016 chr17 81195210 3018318 0.03717359681685656 0.2455177293258223 chr18 78077248 4706938 0.060285654535364774 0.6018813341407185 chr19 59128983 3277313 0.0554265071665447 0.5073990420435504 chr20 63025520 4408329 0.06994514285641752 0.30895890062611764 chr21 48129895 2131248 0.04428116869982783 0.2568682268567493 chr22 51304566 1276688 0.02488449078781799 0.18061277291608835 chrMT 16571 10750 0.6487236738881178 1.1004280456235496 chrX 155270560 8189738 0.05274495049158063 0.3026158147310513 chrY 59373566 382706 0.0064457304114090095 0.1272635009956152