BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506342.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 = 15,414,035 number of mapped reads = 10,085,087 (65.43%) number of supplementary alignments = 174,397 (1.13%) number of secondary alignments = 0 number of mapped bases = 784,512,143 bp number of sequenced bases = 784,183,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,495,006 duplication rate = 10.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.568 >>>>>>> ACTG content number of A's = 225,020,028 bp (28.69%) number of C's = 149,083,531 bp (19.01%) number of T's = 219,793,037 bp (28.03%) number of G's = 190,083,379 bp (24.24%) number of N's = 203,801 bp (0.03%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 5,700,542 number of insertions = 65,055 mapped reads with insertion percentage = 0.63% number of deletions = 163,153 mapped reads with deletion percentage = 1.59% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.2534X std coverageData = 1.5224X There is a 13.68% of reference with a coverageData >= 1X There is a 5.6% of reference with a coverageData >= 2X There is a 2.56% of reference with a coverageData >= 3X There is a 1.27% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 56380097 0.22619842138728313 2.5939825166634525 chr2 243199373 65389040 0.26887010107546616 1.6337004878484196 chr3 198022430 46557536 0.23511243650529892 0.7859735976424858 chr4 191154276 47942960 0.25080767745943594 1.438771387042191 chr5 180915260 58520577 0.3234695459078466 0.962666854085617 chr6 171115067 29567863 0.1727952045274891 0.744971738496787 chr7 159138663 41707666 0.26208380297878964 1.90259177980413 chr8 146364022 49729371 0.33976499361297957 2.1323193169491157 chr9 141213431 21122673 0.1495797733290681 1.3986648239792898 chr10 135534747 43545661 0.32128780230799414 1.848163956186583 chr11 135006516 35323290 0.26164137144313837 1.452274630528113 chr12 133851895 33839198 0.25281075026991584 0.8689889900233362 chr13 115169878 16521260 0.14345122428626694 0.6081298374234689 chr14 107349540 24605471 0.2292089095118619 0.9577543541917084 chr15 102531392 29418502 0.2869219019283382 0.9141622040570891 chr16 90354753 27864971 0.30839518757801265 1.24832271528406 chr17 81195210 19767428 0.24345559300850383 1.0346978293458176 chr18 78077248 13873955 0.17769523587716615 2.3372915572951105 chr19 59128983 19937766 0.3371910861379097 2.01563660610158 chr20 63025520 20829763 0.3304972811013697 1.0860318472203345 chr21 48129895 13003376 0.2701725403722572 1.318417618636383 chr22 51304566 9391333 0.18305062750165355 0.7780087416887183 chrMT 16571 38895 2.347172771709613 3.7548199164378695 chrX 155270560 56757070 0.36553658336776784 1.2048251599964646 chrY 59373566 2876421 0.048446155314302665 1.6019958001535963