BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618600.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 45,291,598 number of mapped reads = 43,504,994 (96.06%) number of supplementary alignments = 144,224 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,961,161 number of mapped paired reads (second in pair) = 21,543,833 number of mapped paired reads (both in pair) = 42,851,206 number of mapped paired reads (singletons) = 653,788 number of mapped bases = 4,139,817,961 bp number of sequenced bases = 4,136,528,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,849,581 duplication rate = 23.83% >>>>>>> Insert size mean insert size = 65,959.611 std insert size = 2,550,705.9454 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 52.9089 >>>>>>> ACTG content number of A's = 1,125,555,285 bp (27.21%) number of C's = 906,266,173 bp (21.91%) number of T's = 1,133,664,624 bp (27.41%) number of G's = 970,846,071 bp (23.47%) number of N's = 196,770 bp (0%) GC percentage = 45.38% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 66,176,897 number of insertions = 793,487 mapped reads with insertion percentage = 1.79% number of deletions = 2,478,999 mapped reads with deletion percentage = 5.54% homopolymer indels = 53.41% >>>>>>> Coverage mean coverageData = 1.3373X std coverageData = 5.377X There is a 24.78% of reference with a coverageData >= 1X There is a 17.05% of reference with a coverageData >= 2X There is a 12.74% of reference with a coverageData >= 3X There is a 9.99% of reference with a coverageData >= 4X There is a 8.05% of reference with a coverageData >= 5X There is a 6.64% of reference with a coverageData >= 6X There is a 5.56% of reference with a coverageData >= 7X There is a 4.73% of reference with a coverageData >= 8X There is a 4.06% of reference with a coverageData >= 9X There is a 3.52% of reference with a coverageData >= 10X There is a 3.08% of reference with a coverageData >= 11X There is a 2.71% of reference with a coverageData >= 12X There is a 2.4% of reference with a coverageData >= 13X There is a 2.14% of reference with a coverageData >= 14X There is a 1.91% of reference with a coverageData >= 15X There is a 1.72% of reference with a coverageData >= 16X There is a 1.55% of reference with a coverageData >= 17X There is a 1.4% of reference with a coverageData >= 18X There is a 1.27% of reference with a coverageData >= 19X There is a 1.16% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 0.97% of reference with a coverageData >= 22X There is a 0.89% of reference with a coverageData >= 23X There is a 0.82% of reference with a coverageData >= 24X There is a 0.76% of reference with a coverageData >= 25X There is a 0.7% of reference with a coverageData >= 26X There is a 0.65% of reference with a coverageData >= 27X There is a 0.6% of reference with a coverageData >= 28X There is a 0.56% of reference with a coverageData >= 29X There is a 0.52% of reference with a coverageData >= 30X There is a 0.48% of reference with a coverageData >= 31X There is a 0.45% of reference with a coverageData >= 32X There is a 0.42% of reference with a coverageData >= 33X There is a 0.39% of reference with a coverageData >= 34X There is a 0.37% of reference with a coverageData >= 35X There is a 0.34% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.3% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 376864942 1.5119919881764308 6.583092804135293 chr2 243199373 359395498 1.4777813510234667 5.969394047697761 chr3 198022430 272005353 1.3736088028007736 4.666304264331381 chr4 191154276 217106159 1.1357640725755986 4.3523688395517235 chr5 180915260 242598757 1.3409524271197466 4.521575620178211 chr6 171115067 238466802 1.3936049360282226 4.903063306889669 chr7 159138663 213578727 1.3420920031230876 4.609967507361828 chr8 146364022 212850501 1.4542542497226538 4.893444811177811 chr9 141213431 186223598 1.3187385695628342 5.528711800834824 chr10 135534747 218794378 1.6143046919178592 5.53447545820272 chr11 135006516 215731595 1.597934687833882 6.337096700433602 chr12 133851895 189803656 1.4180124681835846 4.978824303721194 chr13 115169878 115166823 0.9999734739668649 3.8039940012117626 chr14 107349540 140001669 1.3041664547421443 4.859357530465131 chr15 102531392 142722033 1.391983764347996 5.175930613178914 chr16 90354753 148223809 1.6404649902590072 8.24897562511216 chr17 81195210 137340771 1.6914885865804152 6.150975042826961 chr18 78077248 108863592 1.3943062132517785 5.628120168828243 chr19 59128983 90804887 1.535708588121666 6.030115632882958 chr20 63025520 128229201 2.034559984590369 6.511336051255462 chr21 48129895 56603442 1.1760557965065164 7.770338365613391 chr22 51304566 77189424 1.5045332222477041 6.026010036833643 chrMT 16571 19426 1.1722889385070303 3.9225338143583723 chrX 155270560 9169457 0.059054704253014866 1.179773589505721 chrY 59373566 42063461 0.7084543481858576 4.780746947900823