BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006408.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,280,186 number of mapped reads = 6,493,910 (89.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,271,163 number of mapped paired reads (second in pair) = 3,222,747 number of mapped paired reads (both in pair) = 5,997,828 number of mapped paired reads (singletons) = 496,082 number of mapped bases = 251,584,089 bp number of sequenced bases = 251,554,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,777 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 64,894.4059 std insert size = 2,435,312.7795 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 48.4542 >>>>>>> ACTG content number of A's = 70,164,660 bp (27.89%) number of C's = 54,074,151 bp (21.5%) number of T's = 71,364,528 bp (28.37%) number of G's = 55,940,859 bp (22.24%) number of N's = 10,613 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 845,220 number of insertions = 6,971 mapped reads with insertion percentage = 0.11% number of deletions = 22,358 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.05% >>>>>>> Coverage mean coverageData = 0.0813X std coverageData = 0.4267X There is a 6.72% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 20142999 0.08081423797134692 0.5736317176591395 chr2 243199373 21269200 0.08745581757729284 0.4218716155743375 chr3 198022430 17045972 0.08608101617579382 0.33816307081634195 chr4 191154276 16136454 0.08441586731755872 0.36247275579133503 chr5 180915260 15303678 0.08459031040278195 0.33597551665987063 chr6 171115067 14421683 0.08428061451771515 0.376535508455365 chr7 159138663 13554249 0.08517257053994477 0.48710040901798646 chr8 146364022 12568253 0.08586982530447271 0.7487780219462058 chr9 141213431 10082931 0.07140206798034672 0.36302297936463834 chr10 135534747 11874063 0.08760899520474996 0.4577468215008036 chr11 135006516 11999455 0.08888056188339828 0.40698547131683804 chr12 133851895 11330468 0.0846492909196392 0.3404060169640352 chr13 115169878 8062383 0.0700042679562446 0.30617205448160456 chr14 107349540 7501685 0.06988092356986346 0.3287986019021108 chr15 102531392 7490233 0.07305307041964279 0.31381188016989486 chr16 90354753 7594824 0.08405561133015327 0.40030701846534505 chr17 81195210 7191962 0.08857618571341831 0.36937472111974756 chr18 78077248 6782880 0.08687396359051999 0.5897892442252882 chr19 59128983 5098297 0.086223316237318 0.4629888702091026 chr20 63025520 5656804 0.08975418211543515 0.3559685430726102 chr21 48129895 3203168 0.06655256571825058 0.3447258591704273 chr22 51304566 3055013 0.05954661033483842 0.29359547324964047 chrMT 16571 2979 0.17977189065234445 0.5904649155295728 chrX 155270560 13634546 0.08781153362234283 0.37783983447822383 chrY 59373566 579910 0.009767141155038591 0.20669134472309092