BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081172.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 = 2,310,221 number of mapped reads = 2,117,730 (91.67%) number of supplementary alignments = 21,222 (0.92%) number of secondary alignments = 0 number of mapped bases = 144,852,820 bp number of sequenced bases = 144,796,922 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,867 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4806 >>>>>>> ACTG content number of A's = 42,101,385 bp (29.08%) number of C's = 27,007,894 bp (18.65%) number of T's = 45,213,427 bp (31.23%) number of G's = 30,430,918 bp (21.02%) number of N's = 43,298 bp (0.03%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,204,809 number of insertions = 11,340 mapped reads with insertion percentage = 0.53% number of deletions = 34,396 mapped reads with deletion percentage = 1.61% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.0468X std coverageData = 0.3888X There is a 4.1% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 12025458 0.048246451510345484 0.7260813560125433 chr2 243199373 11544636 0.04746984277792526 0.4027363148828176 chr3 198022430 9525206 0.048101651918926555 0.24144136346009437 chr4 191154276 11066733 0.05789424768086276 0.27096907092265027 chr5 180915260 8548562 0.04725174648064514 0.2419868855557277 chr6 171115067 9233557 0.0539610985863682 0.316361433562869 chr7 159138663 8204846 0.05155784172951108 0.5380202830771963 chr8 146364022 7387853 0.050475881292740096 0.5944070585267521 chr9 141213431 5920093 0.04192301651533415 0.3271715909874815 chr10 135534747 6742888 0.04975025334278301 0.3351309812969877 chr11 135006516 6387357 0.047311471988507575 0.3361531043649384 chr12 133851895 7033497 0.052546861589072014 0.25759099069541147 chr13 115169878 5003185 0.04344178431794466 0.22927179756892402 chr14 107349540 4197517 0.039101397174128555 0.23013912722170596 chr15 102531392 3732511 0.03640359237490894 0.21390788322275428 chr16 90354753 3287118 0.03638013376009118 0.24114736480952906 chr17 81195210 3235897 0.039853299227873173 0.25696634567456283 chr18 78077248 3828950 0.049040534830325985 0.6119614095287715 chr19 59128983 2543156 0.043010311880385295 0.46394123386589503 chr20 63025520 2958305 0.046938208522515956 0.24649581889710206 chr21 48129895 1937092 0.04024716862565356 0.23176397496586024 chr22 51304566 1247310 0.02431187118900879 0.16962707503008925 chrMT 16571 1909 0.115201255204876 0.35455098784511924 chrX 155270560 8941398 0.057585919700424856 0.29611612240059326 chrY 59373566 317786 0.005352314530004817 0.11234976101973496