BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089586.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 22,640,150 number of mapped reads = 17,805,029 (78.64%) number of supplementary alignments = 715 (0%) number of secondary alignments = 0 number of mapped bases = 835,988,992 bp number of sequenced bases = 835,815,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,836,704 duplication rate = 7.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6258 >>>>>>> ACTG content number of A's = 257,303,566 bp (30.78%) number of C's = 169,305,258 bp (20.26%) number of T's = 228,175,094 bp (27.3%) number of G's = 180,818,675 bp (21.63%) number of N's = 213,401 bp (0.03%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 5,086,286 number of insertions = 38,008 mapped reads with insertion percentage = 0.21% number of deletions = 115,723 mapped reads with deletion percentage = 0.65% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.27X std coverageData = 1.3891X There is a 14.88% of reference with a coverageData >= 1X There is a 5.72% of reference with a coverageData >= 2X There is a 2.62% of reference with a coverageData >= 3X There is a 1.34% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 65162580 0.26143397251555894 1.978510654031535 chr2 243199373 69413511 0.28541813304757163 1.6531503834243149 chr3 198022430 56900874 0.28734560019286703 0.9065803943047392 chr4 191154276 52077738 0.27243825819517636 0.9576554929544963 chr5 180915260 52040298 0.28765012967949743 0.9228434667050377 chr6 171115067 49286590 0.2880318540272085 1.101960531906137 chr7 159138663 46547162 0.2924943638617851 1.9192040892138715 chr8 146364022 41814901 0.28569111745234765 2.383972890075628 chr9 141213431 35284924 0.24986946177945354 1.2904237504246152 chr10 135534747 38854583 0.2866761761100273 1.287055658814136 chr11 135006516 38310928 0.2837709551737488 1.3248821126829864 chr12 133851895 38800374 0.2898754179012557 0.9719736474534093 chr13 115169878 27683998 0.24037533494652136 0.8374328117655035 chr14 107349540 26002924 0.2422266923547134 1.0406482327346154 chr15 102531392 24053627 0.23459768301985015 0.8292985834440341 chr16 90354753 22713241 0.25137848586670364 0.9667856614955521 chr17 81195210 22257996 0.2741294221666524 1.0567184258410576 chr18 78077248 22111956 0.28320613964262675 2.0984796273486235 chr19 59128983 16362676 0.2767285207662036 1.8656956599728716 chr20 63025520 17554782 0.2785345047529953 0.9829124466598983 chr21 48129895 10990382 0.22834834773688992 0.9741482605155289 chr22 51304566 9347893 0.18220391923790955 0.7265453056834055 chrMT 16571 225767 13.62422304025104 12.624162765980163 chrX 155270560 49706341 0.3201272733221288 1.232406741720206 chrY 59373566 2482946 0.04181904789077348 0.5822479891907115