BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960907.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 84,324,010 number of mapped reads = 79,296,825 (94.04%) number of supplementary alignments = 1,376,968 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 39,731,274 number of mapped paired reads (second in pair) = 39,565,551 number of mapped paired reads (both in pair) = 77,889,248 number of mapped paired reads (singletons) = 1,407,577 number of mapped bases = 7,012,665,483 bp number of sequenced bases = 7,010,701,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,547,142 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 159,131.7732 std insert size = 4,147,371.2887 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.438 >>>>>>> ACTG content number of A's = 2,027,250,245 bp (28.92%) number of C's = 1,447,498,254 bp (20.65%) number of T's = 2,062,187,550 bp (29.41%) number of G's = 1,472,986,895 bp (21.01%) number of N's = 778,960 bp (0.01%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 105,736,839 number of insertions = 1,119,064 mapped reads with insertion percentage = 1.38% number of deletions = 920,587 mapped reads with deletion percentage = 1.13% homopolymer indels = 37.29% >>>>>>> Coverage mean coverageData = 2.2653X std coverageData = 31.9401X There is a 73.94% of reference with a coverageData >= 1X There is a 54.27% of reference with a coverageData >= 2X There is a 35.53% of reference with a coverageData >= 3X There is a 21.98% of reference with a coverageData >= 4X There is a 12.81% of reference with a coverageData >= 5X There is a 7.24% of reference with a coverageData >= 6X There is a 3.99% of reference with a coverageData >= 7X There is a 2.19% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.69% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 648164099 2.600451290350045 78.19296849445959 chr2 243199373 608492335 2.502030854331191 50.96455145569114 chr3 198022430 481433866 2.431208757512975 5.317755381324918 chr4 191154276 422400492 2.2097360354104767 14.486123670792683 chr5 180915260 340715758 1.883289215072294 3.285261834135102 chr6 171115067 348307416 2.035515762033977 9.496353873408175 chr7 159138663 396597171 2.4921484416392263 20.053632954854415 chr8 146364022 363606477 2.4842613097910085 24.991818380167906 chr9 141213431 334988110 2.3722113939714418 24.320312758723777 chr10 135534747 341222373 2.5176006932008366 53.551291407379104 chr11 135006516 317805182 2.3539988395819353 15.695553222538841 chr12 133851895 262384357 1.9602588144157391 3.1040753497810796 chr13 115169878 217930117 1.89224926503786 2.1920940620544753 chr14 107349540 154629826 1.4404330563503114 13.578911073784006 chr15 102531392 183617398 1.79084077976821 2.4760055523439037 chr16 90354753 248788614 2.753464601911977 26.266258819801337 chr17 81195210 141987738 1.7487206203420127 7.816346930808746 chr18 78077248 270463727 3.464053023487713 29.41323991290726 chr19 59128983 143852873 2.4328656726600557 36.401938687591816 chr20 63025520 132771291 2.106627458210579 6.684975829105035 chr21 48129895 98785365 2.0524741431494915 9.545063829739817 chr22 51304566 75371819 1.4691054788378874 2.3532582954098937 chrMT 16571 1500099 90.52555669543177 19.796022448851602 chrX 155270560 454749357 2.928754536597279 10.368515211475463 chrY 59373566 22099623 0.3722131663777783 17.431192516463575