BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081228.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 = 2,086,921 number of mapped reads = 1,833,343 (87.85%) number of supplementary alignments = 22,717 (1.09%) number of secondary alignments = 0 number of mapped bases = 119,401,600 bp number of sequenced bases = 119,356,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,853 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2207 >>>>>>> ACTG content number of A's = 33,987,736 bp (28.48%) number of C's = 22,993,981 bp (19.26%) number of T's = 36,617,356 bp (30.68%) number of G's = 25,742,449 bp (21.57%) number of N's = 15,092 bp (0.01%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,032,583 number of insertions = 8,969 mapped reads with insertion percentage = 0.49% number of deletions = 27,184 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.95% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.2967X There is a 3.17% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 11786034 0.04728587617039478 0.4521081828721961 chr2 243199373 8048198 0.03309300472579754 0.30794114306751186 chr3 198022430 8575458 0.043305488171213734 0.24812950408943477 chr4 191154276 5890581 0.030815847404846962 0.21180922855429024 chr5 180915260 6608620 0.03652881465057176 0.22499543608732595 chr6 171115067 9172631 0.0536050457789319 0.2999956468051215 chr7 159138663 6537736 0.04108200909039936 0.4328676027471852 chr8 146364022 7362115 0.05030003206662358 0.36085541184021774 chr9 141213431 3094065 0.021910557502140146 0.2175488163261654 chr10 135534747 3516504 0.02594540571946469 0.28777684296574985 chr11 135006516 6396697 0.04738065383451566 0.3157284022922099 chr12 133851895 3039179 0.022705535846167885 0.18140636066645166 chr13 115169878 3105554 0.026964984715882045 0.19353158252638855 chr14 107349540 5188535 0.04833309020234274 0.26378431037033945 chr15 102531392 2438057 0.02377863942391419 0.1860902203946742 chr16 90354753 4138784 0.04580593563240663 0.25998030148881146 chr17 81195210 1921247 0.02366207316909458 0.19323131511430217 chr18 78077248 3222212 0.041269538598491584 0.36260792802808234 chr19 59128983 3506786 0.0593073958332752 0.39613960996124253 chr20 63025520 2937419 0.04660681895206894 0.25560745331411583 chr21 48129895 2061320 0.04282826713002386 0.25049785121430435 chr22 51304566 1033926 0.020152709215004373 0.16404940833416012 chrMT 16571 49082 2.9619214290024742 2.7608933840347833 chrX 155270560 9437107 0.06077846953086277 0.3064874347349529 chrY 59373566 333753 0.005621238919690288 0.10845241281096717