BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504669.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 98,706,562 number of mapped reads = 98,195,689 (99.48%) number of supplementary alignments = 1,003,052 (1.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 49,203,782 number of mapped paired reads (second in pair) = 48,991,907 number of mapped paired reads (both in pair) = 97,942,576 number of mapped paired reads (singletons) = 253,113 number of mapped bases = 9,319,388,247 bp number of sequenced bases = 9,310,997,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,698,422 duplication rate = 24.57% >>>>>>> Insert size mean insert size = 34,904.5816 std insert size = 1,833,314.758 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 51.1335 >>>>>>> ACTG content number of A's = 2,853,497,268 bp (30.65%) number of C's = 1,796,664,769 bp (19.3%) number of T's = 2,876,392,624 bp (30.89%) number of G's = 1,779,207,260 bp (19.11%) number of N's = 5,235,905 bp (0.06%) GC percentage = 38.4% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 98,129,540 number of insertions = 3,143,917 mapped reads with insertion percentage = 3.13% number of deletions = 3,188,877 mapped reads with deletion percentage = 3.17% homopolymer indels = 38.37% >>>>>>> Coverage mean coverageData = 3.0104X std coverageData = 157.876X There is a 29.87% of reference with a coverageData >= 1X There is a 21.07% of reference with a coverageData >= 2X There is a 14.96% of reference with a coverageData >= 3X There is a 11.77% of reference with a coverageData >= 4X There is a 9.56% of reference with a coverageData >= 5X There is a 8.01% of reference with a coverageData >= 6X There is a 6.84% of reference with a coverageData >= 7X There is a 5.95% of reference with a coverageData >= 8X There is a 5.23% of reference with a coverageData >= 9X There is a 4.65% of reference with a coverageData >= 10X There is a 4.16% of reference with a coverageData >= 11X There is a 3.76% of reference with a coverageData >= 12X There is a 3.42% of reference with a coverageData >= 13X There is a 3.12% of reference with a coverageData >= 14X There is a 2.87% of reference with a coverageData >= 15X There is a 2.65% of reference with a coverageData >= 16X There is a 2.45% of reference with a coverageData >= 17X There is a 2.28% of reference with a coverageData >= 18X There is a 2.12% of reference with a coverageData >= 19X There is a 1.98% of reference with a coverageData >= 20X There is a 1.86% of reference with a coverageData >= 21X There is a 1.75% of reference with a coverageData >= 22X There is a 1.64% of reference with a coverageData >= 23X There is a 1.55% of reference with a coverageData >= 24X There is a 1.47% of reference with a coverageData >= 25X There is a 1.39% of reference with a coverageData >= 26X There is a 1.32% of reference with a coverageData >= 27X There is a 1.25% of reference with a coverageData >= 28X There is a 1.19% of reference with a coverageData >= 29X There is a 1.14% of reference with a coverageData >= 30X There is a 1.08% of reference with a coverageData >= 31X There is a 1.04% of reference with a coverageData >= 32X There is a 0.99% of reference with a coverageData >= 33X There is a 0.95% of reference with a coverageData >= 34X There is a 0.91% of reference with a coverageData >= 35X There is a 0.87% of reference with a coverageData >= 36X There is a 0.84% of reference with a coverageData >= 37X There is a 0.8% of reference with a coverageData >= 38X There is a 0.77% of reference with a coverageData >= 39X There is a 0.74% of reference with a coverageData >= 40X There is a 0.72% of reference with a coverageData >= 41X There is a 0.69% of reference with a coverageData >= 42X There is a 0.67% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.62% of reference with a coverageData >= 45X There is a 0.6% of reference with a coverageData >= 46X There is a 0.58% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.53% of reference with a coverageData >= 50X There is a 0.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 556553283 2.2329063043738615 11.500889108197535 chr2 243199373 720439561 2.96234135850342 22.9294368311254 chr3 198022430 1793345802 9.05627610973161 466.33629063632435 chr4 191154276 465864964 2.437115055694595 12.658471199129037 chr5 180915260 448370838 2.4783472549524013 16.149210227834722 chr6 171115067 409680447 2.3941810279044566 37.48846633320195 chr7 159138663 416121745 2.614837508091921 12.795206312552585 chr8 146364022 994171723 6.7924597139042815 300.16118259738965 chr9 141213431 251380273 1.7801442201344149 9.345677747102037 chr10 135534747 292881929 2.160936110354048 11.530896439890299 chr11 135006516 290343342 2.1505876205264047 10.870342260799648 chr12 133851895 838577778 6.264967544912233 324.61837586682407 chr13 115169878 526549134 4.57193446015459 230.2245954275242 chr14 107349540 211264875 1.9680091316646535 9.244271927781968 chr15 102531392 181558727 1.7707623339396388 8.796488873843929 chr16 90354753 165949885 1.8366480953138127 10.98233321003522 chr17 81195210 148041595 1.8232799077679582 19.754818754001228 chr18 78077248 164603234 2.1082099871143 7.260277707781111 chr19 59128983 73678103 1.2460573353680038 6.372477577200603 chr20 63025520 123753756 1.9635499397704295 10.781810152215796 chr21 48129895 94717211 1.967949670365996 11.418417099466158 chr22 51304566 47725244 0.9302338509207932 7.862012383054559 chrMT 16571 8310 0.5014784865125822 1.9517244959096796 chrX 155270560 30283613 0.19503770064331577 12.904470718406575 chrY 59373566 73522875 1.2383099071394836 20.489077266183006