BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708646.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,815,581 number of mapped reads = 3,673,920 (96.29%) number of supplementary alignments = 132 (0%) number of secondary alignments = 0 number of mapped bases = 183,235,300 bp number of sequenced bases = 183,217,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,100 duplication rate = 0.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3919 >>>>>>> ACTG content number of A's = 56,710,072 bp (30.95%) number of C's = 34,780,560 bp (18.98%) number of T's = 56,653,744 bp (30.92%) number of G's = 35,066,913 bp (19.14%) number of N's = 5,991 bp (0%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 301,154 number of insertions = 12,907 mapped reads with insertion percentage = 0.35% number of deletions = 10,512 mapped reads with deletion percentage = 0.29% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.2693X There is a 5.22% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0% 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 11087097 0.04448172267542715 0.2322366358582061 chr2 243199373 17212688 0.07077603773263018 0.29681801410869385 chr3 198022430 18985505 0.0958755278379323 0.34900239313976444 chr4 191154276 15148384 0.07924690107376933 0.3090898930306514 chr5 180915260 11652846 0.0644105201518103 0.27893261790918117 chr6 171115067 11845900 0.06922768525111818 0.28722253163290046 chr7 159138663 8388577 0.05271237574743229 0.25167029381013634 chr8 146364022 13979355 0.09551086946763461 0.34503254864572236 chr9 141213431 6688875 0.04736713039710791 0.23776863995196862 chr10 135534747 8400088 0.061977376177933176 0.27372811965506333 chr11 135006516 8661321 0.06415483679321078 0.2807293700324767 chr12 133851895 7113017 0.05314095104891866 0.24953654590347862 chr13 115169878 7739190 0.06719803940401847 0.2903514360463601 chr14 107349540 6842449 0.06373990051564264 0.27890327326045844 chr15 102531392 2978533 0.029049961596151936 0.18809996644008228 chr16 90354753 3822087 0.04230089589199585 0.22107641347661383 chr17 81195210 3192158 0.03931460981503712 0.21565831083766415 chr18 78077248 7609036 0.09745522793016476 0.3444019918664868 chr19 59128983 1422383 0.024055597235623012 0.16485012258985143 chr20 63025520 2765728 0.04388266848095819 0.2258284316068224 chr21 48129895 1741345 0.03618011217352542 0.2062228100184449 chr22 51304566 1343883 0.026194218268993836 0.17653700980915663 chrMT 16571 738 0.04453563454227265 0.2176692970073702 chrX 155270560 4333826 0.027911446960711676 0.18044195322546644 chrY 59373566 280291 0.004720804541199362 0.07172646369835235