BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365353.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 556,620,444 number of mapped reads = 537,586,567 (96.58%) number of supplementary alignments = 2,378,614 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 269,306,503 number of mapped paired reads (second in pair) = 268,280,064 number of mapped paired reads (both in pair) = 535,231,272 number of mapped paired reads (singletons) = 2,355,295 number of mapped bases = 56,000,917,460 bp number of sequenced bases = 55,982,396,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 328,396,002 duplication rate = 31.98% >>>>>>> Insert size mean insert size = 56,821.0922 std insert size = 2,341,332.1983 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 53.8541 >>>>>>> ACTG content number of A's = 16,670,234,606 bp (29.78%) number of C's = 11,143,411,134 bp (19.91%) number of T's = 16,191,102,822 bp (28.92%) number of G's = 11,971,106,012 bp (21.38%) number of N's = 6,541,789 bp (0.01%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 274,127,294 number of insertions = 16,062,270 mapped reads with insertion percentage = 2.92% number of deletions = 8,796,880 mapped reads with deletion percentage = 1.6% homopolymer indels = 50.42% >>>>>>> Coverage mean coverageData = 18.0899X std coverageData = 160.1927X There is a 76.23% of reference with a coverageData >= 1X There is a 73.88% of reference with a coverageData >= 2X There is a 70.75% of reference with a coverageData >= 3X There is a 68.46% of reference with a coverageData >= 4X There is a 65.69% of reference with a coverageData >= 5X There is a 63.41% of reference with a coverageData >= 6X There is a 60.83% of reference with a coverageData >= 7X There is a 58.6% of reference with a coverageData >= 8X There is a 56.16% of reference with a coverageData >= 9X There is a 54% of reference with a coverageData >= 10X There is a 51.69% of reference with a coverageData >= 11X There is a 49.62% of reference with a coverageData >= 12X There is a 47.44% of reference with a coverageData >= 13X There is a 45.45% of reference with a coverageData >= 14X There is a 43.4% of reference with a coverageData >= 15X There is a 41.53% of reference with a coverageData >= 16X There is a 39.61% of reference with a coverageData >= 17X There is a 37.85% of reference with a coverageData >= 18X There is a 36.08% of reference with a coverageData >= 19X There is a 34.44% of reference with a coverageData >= 20X There is a 32.8% of reference with a coverageData >= 21X There is a 31.28% of reference with a coverageData >= 22X There is a 29.77% of reference with a coverageData >= 23X There is a 28.38% of reference with a coverageData >= 24X There is a 27% of reference with a coverageData >= 25X There is a 25.73% of reference with a coverageData >= 26X There is a 24.47% of reference with a coverageData >= 27X There is a 23.31% of reference with a coverageData >= 28X There is a 22.16% of reference with a coverageData >= 29X There is a 21.1% of reference with a coverageData >= 30X There is a 20.06% of reference with a coverageData >= 31X There is a 19.09% of reference with a coverageData >= 32X There is a 18.14% of reference with a coverageData >= 33X There is a 17.26% of reference with a coverageData >= 34X There is a 16.4% of reference with a coverageData >= 35X There is a 15.59% of reference with a coverageData >= 36X There is a 14.81% of reference with a coverageData >= 37X There is a 14.08% of reference with a coverageData >= 38X There is a 13.37% of reference with a coverageData >= 39X There is a 12.71% of reference with a coverageData >= 40X There is a 12.07% of reference with a coverageData >= 41X There is a 11.47% of reference with a coverageData >= 42X There is a 10.89% of reference with a coverageData >= 43X There is a 10.34% of reference with a coverageData >= 44X There is a 9.81% of reference with a coverageData >= 45X There is a 9.32% of reference with a coverageData >= 46X There is a 8.85% of reference with a coverageData >= 47X There is a 8.4% of reference with a coverageData >= 48X There is a 7.97% of reference with a coverageData >= 49X There is a 7.57% of reference with a coverageData >= 50X There is a 7.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4841113330 19.422673093360117 432.2276258482423 chr2 243199373 4916946946 20.217761605824535 104.54897533709546 chr3 198022430 3765831668 19.01719753666289 30.805746452405433 chr4 191154276 3550444732 18.57371337065983 80.18379469682502 chr5 180915260 3458111908 19.114539635849404 23.088144718068833 chr6 171115067 3347789950 19.564553891680386 55.610623174097 chr7 159138663 3017482085 18.961338672299892 115.95533081787997 chr8 146364022 2824669988 19.298936647149528 48.3208442759004 chr9 141213431 2379511333 16.85046044239234 136.70787858603163 chr10 135534747 2912771016 21.49095402081652 321.01962858604986 chr11 135006516 2626355644 19.45354729396913 90.36969509907463 chr12 133851895 2647981614 19.782922117015975 37.3752426017089 chr13 115169878 1784209406 15.49197964766447 20.069497015554543 chr14 107349540 1758398357 16.380120091804773 24.23369978808112 chr15 102531392 1687090494 16.454380079029846 25.676179821820853 chr16 90354753 1630491447 18.045441914937225 56.170442658656526 chr17 81195210 1695521862 20.88204294317362 72.16367251530606 chr18 78077248 1465073912 18.764415364639902 157.81178959598188 chr19 59128983 1183076042 20.00839490170159 221.40684101008085 chr20 63025520 1163447293 18.459939608590297 31.395034191006307 chr21 48129895 736510641 15.302560726550515 51.33305142846073 chr22 51304566 725280618 14.136765487890493 41.025149862802515 chrMT 16571 61740612 3725.82294369682 705.9983097870029 chrX 155270560 1390708431 8.956678142978296 36.42368500981959 chrY 59373566 430358131 7.24831200133743 149.3056591934757