BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708520.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,380,389 number of mapped reads = 2,371,320 (70.15%) number of supplementary alignments = 629 (0.02%) number of secondary alignments = 0 number of mapped bases = 113,854,085 bp number of sequenced bases = 113,833,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,937 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1024 >>>>>>> ACTG content number of A's = 32,947,858 bp (28.94%) number of C's = 21,215,905 bp (18.64%) number of T's = 36,307,716 bp (31.9%) number of G's = 23,359,931 bp (20.52%) number of N's = 1,695 bp (0%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 540,819 number of insertions = 5,325 mapped reads with insertion percentage = 0.22% number of deletions = 13,719 mapped reads with deletion percentage = 0.58% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3174X There is a 3.22% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 9569765 0.038394147070149126 0.5427310909236303 chr2 243199373 10377372 0.04267022514075314 0.31083531037501483 chr3 198022430 7838346 0.03958312197259674 0.2234358891606913 chr4 191154276 6274184 0.03282261914978036 0.20779135303434537 chr5 180915260 7394175 0.04087093040133817 0.2273880780984187 chr6 171115067 7320516 0.042781247311202586 0.27203383435204664 chr7 159138663 6542304 0.04111071361709254 0.3742514320729392 chr8 146364022 5886650 0.040219241857127976 0.6015244006960849 chr9 141213431 4826147 0.03417626047199434 0.25232432969789903 chr10 135534747 5543712 0.0409025148362877 0.26331071283147667 chr11 135006516 5458040 0.040427974602351785 0.29769810684602305 chr12 133851895 5174379 0.03865749528611455 0.22333714516200676 chr13 115169878 3902627 0.03388583080725326 0.20669800911866898 chr14 107349540 3708726 0.03454813127284942 0.21485144470085024 chr15 102531392 3301975 0.03220452717544301 0.2029690148633338 chr16 90354753 3026016 0.03349039092608665 0.21021513080740548 chr17 81195210 3031132 0.037331414008289404 0.2504818220349633 chr18 78077248 3113798 0.03988099068245848 0.4313007343160412 chr19 59128983 2008047 0.033960452186366875 0.3840249073977118 chr20 63025520 2410713 0.0382497915130252 0.2200463987003783 chr21 48129895 1557177 0.03235363384856751 0.22147490748512652 chr22 51304566 1269035 0.024735322778093476 0.18500321668128203 chrMT 16571 148865 8.983465089614386 6.804609602521349 chrX 155270560 3512507 0.022621847953662302 0.19384416972500473 chrY 59373566 657877 0.011080301290981916 0.1267380107873466