BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153396.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 = 36,180,632 number of mapped reads = 35,874,962 (99.16%) number of supplementary alignments = 236,399 (0.65%) number of secondary alignments = 0 number of mapped bases = 3,069,471,919 bp number of sequenced bases = 3,068,889,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,012,018 duplication rate = 42.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6178 >>>>>>> ACTG content number of A's = 819,898,567 bp (26.72%) number of C's = 720,671,538 bp (23.48%) number of T's = 848,743,443 bp (27.66%) number of G's = 678,338,554 bp (22.1%) number of N's = 1,236,993 bp (0.04%) GC percentage = 45.59% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 6,997,836 number of insertions = 337,172 mapped reads with insertion percentage = 0.93% number of deletions = 283,406 mapped reads with deletion percentage = 0.78% homopolymer indels = 49.62% >>>>>>> Coverage mean coverageData = 0.9915X std coverageData = 10.8474X There is a 14.74% of reference with a coverageData >= 1X There is a 10.37% of reference with a coverageData >= 2X There is a 4.2% of reference with a coverageData >= 3X There is a 3.27% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 1.87% of reference with a coverageData >= 6X There is a 1.59% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.34% of reference with a coverageData >= 9X There is a 1.26% of reference with a coverageData >= 10X There is a 1.19% of reference with a coverageData >= 11X There is a 1.13% of reference with a coverageData >= 12X There is a 1.08% of reference with a coverageData >= 13X There is a 1.03% of reference with a coverageData >= 14X There is a 0.99% of reference with a coverageData >= 15X There is a 0.96% of reference with a coverageData >= 16X There is a 0.92% of reference with a coverageData >= 17X There is a 0.89% of reference with a coverageData >= 18X There is a 0.86% of reference with a coverageData >= 19X There is a 0.83% of reference with a coverageData >= 20X There is a 0.81% of reference with a coverageData >= 21X There is a 0.78% of reference with a coverageData >= 22X There is a 0.76% of reference with a coverageData >= 23X There is a 0.74% of reference with a coverageData >= 24X There is a 0.72% of reference with a coverageData >= 25X There is a 0.7% of reference with a coverageData >= 26X There is a 0.68% of reference with a coverageData >= 27X There is a 0.66% of reference with a coverageData >= 28X There is a 0.64% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.61% of reference with a coverageData >= 31X There is a 0.59% of reference with a coverageData >= 32X There is a 0.58% of reference with a coverageData >= 33X There is a 0.57% of reference with a coverageData >= 34X There is a 0.55% of reference with a coverageData >= 35X There is a 0.54% of reference with a coverageData >= 36X There is a 0.53% of reference with a coverageData >= 37X There is a 0.51% of reference with a coverageData >= 38X There is a 0.5% of reference with a coverageData >= 39X There is a 0.49% of reference with a coverageData >= 40X There is a 0.48% of reference with a coverageData >= 41X There is a 0.47% of reference with a coverageData >= 42X There is a 0.46% of reference with a coverageData >= 43X There is a 0.45% of reference with a coverageData >= 44X There is a 0.44% of reference with a coverageData >= 45X There is a 0.43% of reference with a coverageData >= 46X There is a 0.42% of reference with a coverageData >= 47X There is a 0.42% of reference with a coverageData >= 48X There is a 0.41% of reference with a coverageData >= 49X There is a 0.4% of reference with a coverageData >= 50X There is a 0.39% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 334947616 1.3438185816997423 14.100656253017927 chr2 243199373 248521669 1.021884497210443 10.534984204470225 chr3 198022430 177004449 0.8938606045789863 9.212782278700073 chr4 191154276 141161183 0.7384673048067206 8.081958268943362 chr5 180915260 156673750 0.8660062727710199 9.080964410040288 chr6 171115067 176880170 1.03369138148425 13.344751666633874 chr7 159138663 160406628 1.007967674078046 10.552994279100531 chr8 146364022 122855541 0.839383472257957 10.334347301302556 chr9 141213431 121378855 0.8595418590176455 9.285563284869392 chr10 135534747 129085651 0.9524173974368358 9.8070685831044 chr11 135006516 152278095 1.1279314473976945 10.750658022076141 chr12 133851895 167841799 1.2539366663430502 12.548213318869317 chr13 115169878 64097394 0.5565465129693026 6.573606874010773 chr14 107349540 91148200 0.8490786266992854 8.886955925146049 chr15 102531392 118050502 1.151359595313014 11.664996076781877 chr16 90354753 98787832 1.0933329871423587 9.990438880113208 chr17 81195210 122086218 1.5036135506023076 12.959634341723401 chr18 78077248 56054070 0.7179309137535176 7.88217987026726 chr19 59128983 115234877 1.9488729748658116 17.019357644213443 chr20 63025520 60353657 0.9576066488622387 9.735451167094007 chr21 48129895 28994488 0.6024215926504722 7.625202803764189 chr22 51304566 45830702 0.8933064943966196 10.338285575158027 chrMT 16571 4004 0.24162693862772314 0.6990828123856896 chrX 155270560 177331386 1.142079902333063 14.137680138323935 chrY 59373566 2463183 0.04148618932539777 1.8816593429941593