BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006162.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 = 4,856,636 number of mapped reads = 4,107,233 (84.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,056,476 number of mapped paired reads (second in pair) = 2,050,757 number of mapped paired reads (both in pair) = 3,842,048 number of mapped paired reads (singletons) = 265,185 number of mapped bases = 158,527,061 bp number of sequenced bases = 158,507,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,951 duplication rate = 4.48% >>>>>>> Insert size mean insert size = 52,353.8089 std insert size = 2,189,638.9684 median insert size = 75 >>>>>>> Mapping quality mean mapping quality = 46.6715 >>>>>>> ACTG content number of A's = 42,258,149 bp (26.66%) number of C's = 36,232,513 bp (22.86%) number of T's = 42,848,167 bp (27.03%) number of G's = 37,149,438 bp (23.44%) number of N's = 19,392 bp (0.01%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 596,743 number of insertions = 5,567 mapped reads with insertion percentage = 0.14% number of deletions = 14,498 mapped reads with deletion percentage = 0.35% homopolymer indels = 38.33% >>>>>>> Coverage mean coverageData = 0.0512X std coverageData = 0.3808X There is a 3.88% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.06% 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% 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 13474404 0.054059660697896514 0.3826682494888367 chr2 243199373 13280238 0.054606382558395825 0.32721935585040635 chr3 198022430 10370281 0.05236922403184326 0.28517149461518143 chr4 191154276 9313271 0.04872122766429771 0.30018917352314245 chr5 180915260 9345632 0.051657510814731716 0.28517741014767917 chr6 171115067 8748051 0.051123791454320035 0.29375187935080543 chr7 159138663 8410567 0.05285055712702576 0.34066860342367755 chr8 146364022 7889966 0.05390645796820205 0.5826578149377069 chr9 141213431 6562467 0.046471974751466805 0.28992231776278 chr10 135534747 7592197 0.05601660952670683 0.3529786932727535 chr11 135006516 7403831 0.05484054562225722 0.3143934143613624 chr12 133851895 7278127 0.05437447859815507 0.30400728895169754 chr13 115169878 4587509 0.039832541977686216 0.2580236762734508 chr14 107349540 4796781 0.0446837592410736 1.0141705600984416 chr15 102531392 4498191 0.04387135405320548 0.2659364165515292 chr16 90354753 5074840 0.05616572268201541 0.3250664238532764 chr17 81195210 4876097 0.06005399825925692 0.32093889128064207 chr18 78077248 4074745 0.05218863502975925 0.36989061446659005 chr19 59128983 3787032 0.06404696661195745 0.3889250926509364 chr20 63025520 3726795 0.05913152323058977 0.3253795020340408 chr21 48129895 1947466 0.04046271033834584 0.29483611850393315 chr22 51304566 2481576 0.04836949600158395 0.45743607668577246 chrMT 16571 2196 0.132520668637982 0.5536229559785774 chrX 155270560 8547425 0.05504858744632595 0.2979837178972886 chrY 59373566 457376 0.007703360785168268 0.20414770878431857