BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695970.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 60,266,000 number of mapped reads = 59,912,022 (99.41%) number of supplementary alignments = 596,045 (0.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,049,017 number of mapped paired reads (second in pair) = 29,863,005 number of mapped paired reads (both in pair) = 59,658,522 number of mapped paired reads (singletons) = 253,500 number of mapped bases = 5,945,494,900 bp number of sequenced bases = 5,944,201,733 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,800,505 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 73,949.8604 std insert size = 2,610,717.94 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.9141 >>>>>>> ACTG content number of A's = 1,759,553,868 bp (29.6%) number of C's = 1,195,714,781 bp (20.12%) number of T's = 1,749,868,006 bp (29.44%) number of G's = 1,230,882,957 bp (20.71%) number of N's = 8,182,121 bp (0.14%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 39,508,837 number of insertions = 557,984 mapped reads with insertion percentage = 0.92% number of deletions = 562,607 mapped reads with deletion percentage = 0.92% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 1.9206X std coverageData = 2.7718X There is a 72.22% of reference with a coverageData >= 1X There is a 48.78% of reference with a coverageData >= 2X There is a 29.98% of reference with a coverageData >= 3X There is a 17.41% of reference with a coverageData >= 4X There is a 9.79% of reference with a coverageData >= 5X There is a 5.44% of reference with a coverageData >= 6X There is a 3.02% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 0.96% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 484244741 1.9428025457156233 2.8842956108004176 chr2 243199373 551173676 2.2663449712101027 2.68088465843134 chr3 198022430 431207596 2.177569460186909 2.0214351392534162 chr4 191154276 400141514 2.093290939513171 2.508797645165108 chr5 180915260 422022866 2.3327101649689475 2.1208703153089847 chr6 171115067 361599475 2.1131948304704227 2.311869360039442 chr7 159138663 322019920 2.0235178172886874 2.0907247078404527 chr8 146364022 305259704 2.08561981167749 2.0524735554440836 chr9 141213431 247300575 1.75125392286517 2.3306167104619693 chr10 135534747 274535079 2.0255697160817365 3.076121110818313 chr11 135006516 281367025 2.0840995926448467 2.1136061722341393 chr12 133851895 282666307 2.1117841252826492 2.0963329756920857 chr13 115169878 193164280 1.6772118140126884 1.9201461013831913 chr14 107349540 191011549 1.7793420353734166 2.0275729326095284 chr15 102531392 182695054 1.7818450567802688 2.1166440514705736 chr16 90354753 144310245 1.5971516739136014 2.6428219028199225 chr17 81195210 135060090 1.6633997251808328 2.319591936252411 chr18 78077248 160967405 2.0616429129264393 2.9150834910360555 chr19 59128983 80644269 1.363870388232451 2.0777236053864727 chr20 63025520 111606445 1.7708135529861555 2.088393142868974 chr21 48129895 76543799 1.5903587364983862 3.236024008043653 chr22 51304566 58654378 1.1432584382450481 1.771602069414792 chrMT 16571 9934130 599.4888660913645 158.27784786851768 chrX 155270560 199341460 1.2838329429609838 1.4822458179171838 chrY 59373566 38023318 0.6404081910795117 2.583078215422361