BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472786.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,283,064 number of mapped reads = 8,879,677 (95.65%) number of supplementary alignments = 30,037 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,458,788 number of mapped paired reads (second in pair) = 4,420,889 number of mapped paired reads (both in pair) = 8,819,364 number of mapped paired reads (singletons) = 60,313 number of mapped bases = 870,712,322 bp number of sequenced bases = 870,600,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,931,414 duplication rate = 43.94% >>>>>>> Insert size mean insert size = 20,786.1623 std insert size = 1,428,906.0089 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 55.019 >>>>>>> ACTG content number of A's = 238,027,855 bp (27.34%) number of C's = 198,623,302 bp (22.81%) number of T's = 236,340,252 bp (27.15%) number of G's = 197,440,527 bp (22.68%) number of N's = 169,027 bp (0.02%) GC percentage = 45.49% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 5,120,378 number of insertions = 49,229 mapped reads with insertion percentage = 0.55% number of deletions = 46,138 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.2813X std coverageData = 10.043X There is a 2.8% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.17% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 111566141 0.44760627095889965 16.559281953200163 chr2 243199373 48587242 0.19978358250125916 7.299858176103018 chr3 198022430 96574760 0.48769606554166617 11.497229137100346 chr4 191154276 30586062 0.16000720799988802 6.386966578390932 chr5 180915260 39095854 0.21610036654729955 7.95799125343817 chr6 171115067 59536407 0.34793199712799106 10.997761752905141 chr7 159138663 27963271 0.1757163876637571 6.165447715251453 chr8 146364022 29953310 0.204649404892686 7.198189931350451 chr9 141213431 61303766 0.4341213549297588 12.117362999106142 chr10 135534747 26982632 0.19908276362518315 8.466347800561095 chr11 135006516 45293313 0.3354898292464639 10.969090565881627 chr12 133851895 49696323 0.3712784417433911 13.225297351617336 chr13 115169878 24666870 0.21417813779398118 10.044237170700997 chr14 107349540 22657455 0.2110624321259318 9.617722835335995 chr15 102531392 19423835 0.18944280986646508 8.525505337588053 chr16 90354753 34350536 0.3801740900116234 10.729764973555984 chr17 81195210 25172756 0.3100275989187047 7.707947023473028 chr18 78077248 15866056 0.20320972378534655 7.8929194282809405 chr19 59128983 19244743 0.32547055646128736 9.072247810296513 chr20 63025520 23659182 0.37539050847973965 12.555655526620084 chr21 48129895 4483340 0.09315083691747093 4.3618504336669535 chr22 51304566 9799346 0.19100338944490827 5.51626666578151 chrMT 16571 5060 0.3053527246394303 0.9218747579893528 chrX 155270560 42767224 0.2754367859560756 9.687574276957623 chrY 59373566 1476838 0.02487366179083803 1.1960467499969842