BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618653.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 = 70,279,999 number of mapped reads = 62,312,541 (88.66%) number of supplementary alignments = 291,600 (0.41%) number of secondary alignments = 0 number of mapped bases = 5,706,728,821 bp number of sequenced bases = 5,702,440,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,947,096 duplication rate = 48.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9758 >>>>>>> ACTG content number of A's = 1,475,818,833 bp (25.88%) number of C's = 1,370,849,989 bp (24.04%) number of T's = 1,770,976,403 bp (31.06%) number of G's = 1,082,935,281 bp (18.99%) number of N's = 1,860,171 bp (0.03%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0174 number of mismatches = 97,167,957 number of insertions = 1,265,960 mapped reads with insertion percentage = 1.98% number of deletions = 2,626,501 mapped reads with deletion percentage = 4.11% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 1.8434X std coverageData = 35.4206X There is a 13.86% of reference with a coverageData >= 1X There is a 9.03% of reference with a coverageData >= 2X There is a 6.71% of reference with a coverageData >= 3X There is a 5.32% of reference with a coverageData >= 4X There is a 4.42% of reference with a coverageData >= 5X There is a 3.79% of reference with a coverageData >= 6X There is a 3.33% of reference with a coverageData >= 7X There is a 2.98% of reference with a coverageData >= 8X There is a 2.7% of reference with a coverageData >= 9X There is a 2.48% of reference with a coverageData >= 10X There is a 2.29% of reference with a coverageData >= 11X There is a 2.13% of reference with a coverageData >= 12X There is a 1.99% of reference with a coverageData >= 13X There is a 1.87% of reference with a coverageData >= 14X There is a 1.76% of reference with a coverageData >= 15X There is a 1.67% of reference with a coverageData >= 16X There is a 1.58% of reference with a coverageData >= 17X There is a 1.51% of reference with a coverageData >= 18X There is a 1.44% of reference with a coverageData >= 19X There is a 1.38% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.27% of reference with a coverageData >= 22X There is a 1.22% of reference with a coverageData >= 23X There is a 1.18% of reference with a coverageData >= 24X There is a 1.13% of reference with a coverageData >= 25X There is a 1.1% of reference with a coverageData >= 26X There is a 1.06% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 0.99% of reference with a coverageData >= 29X There is a 0.97% of reference with a coverageData >= 30X There is a 0.94% of reference with a coverageData >= 31X There is a 0.91% of reference with a coverageData >= 32X There is a 0.89% of reference with a coverageData >= 33X There is a 0.86% of reference with a coverageData >= 34X There is a 0.84% of reference with a coverageData >= 35X There is a 0.82% of reference with a coverageData >= 36X There is a 0.8% of reference with a coverageData >= 37X There is a 0.78% of reference with a coverageData >= 38X There is a 0.76% of reference with a coverageData >= 39X There is a 0.74% of reference with a coverageData >= 40X There is a 0.73% of reference with a coverageData >= 41X There is a 0.71% of reference with a coverageData >= 42X There is a 0.7% of reference with a coverageData >= 43X There is a 0.68% of reference with a coverageData >= 44X There is a 0.67% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.64% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.59% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 532184453 2.1351379220836524 35.29357183488838 chr2 243199373 480165620 1.9743703039892295 58.7222044607738 chr3 198022430 374268985 1.890033290673183 28.4782086923903 chr4 191154276 278682446 1.4578928174225096 26.374436945791047 chr5 180915260 331130412 1.830306697179663 32.687609516644784 chr6 171115067 320800736 1.8747661537017077 27.046860804205007 chr7 159138663 281946508 1.7717033854934423 30.793004935928927 chr8 146364022 288699480 1.9724757222099294 43.383697935797 chr9 141213431 232213131 1.6444124992614901 26.813999462545247 chr10 135534747 286243392 2.1119557776575184 41.827790804296384 chr11 135006516 291170319 2.1567130804264294 29.996879880935314 chr12 133851895 265586367 1.984180851529969 34.0912076018252 chr13 115169878 153762756 1.335095240788568 22.05434454866485 chr14 107349540 165500414 1.541696536380128 26.209510606317313 chr15 102531392 176819534 1.724540460740063 25.66199580307252 chr16 90354753 200845083 2.2228502246030155 58.22483415411639 chr17 81195210 161158722 1.9848304105623964 27.854561141438374 chr18 78077248 143397248 1.8366073558330334 26.947788728079882 chr19 59128983 111685583 1.8888466760877656 32.59108756874629 chr20 63025520 162828679 2.583535669360602 37.61925585514286 chr21 48129895 67611166 1.4047644608408143 32.52009541367568 chr22 51304566 81812539 1.5946444026054134 27.61292162609113 chrMT 16571 3186 0.1922635930239575 1.0723467141114225 chrX 155270560 305158151 1.9653316829668162 32.484425367926576 chrY 59373566 13053911 0.21986065313981645 29.36053465487842