BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084814.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 984,354 number of mapped reads = 906,819 (92.12%) number of supplementary alignments = 8,805 (0.89%) number of secondary alignments = 0 number of mapped bases = 62,668,754 bp number of sequenced bases = 62,644,565 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,206 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.248 >>>>>>> ACTG content number of A's = 17,976,300 bp (28.7%) number of C's = 11,387,624 bp (18.18%) number of T's = 20,232,856 bp (32.3%) number of G's = 13,038,819 bp (20.81%) number of N's = 8,966 bp (0.01%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 493,133 number of insertions = 5,175 mapped reads with insertion percentage = 0.57% number of deletions = 14,673 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.1715X There is a 1.82% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 4993362 0.02003349873298811 0.201306813889134 chr2 243199373 4849038 0.019938530022443765 0.19945240759406335 chr3 198022430 5528147 0.027916771852562357 0.18319653742981928 chr4 191154276 3652511 0.01910766045327702 0.15158413320568015 chr5 180915260 3481556 0.0192441256751918 0.1520617785923764 chr6 171115067 3400722 0.019873889889544326 0.15662894772328143 chr7 159138663 3401195 0.02137252466422946 0.17248831598601783 chr8 146364022 4103244 0.028034512470557826 0.23597517899311213 chr9 141213431 4770034 0.03377889741946713 0.21854838489230088 chr10 135534747 1974811 0.014570514526433579 0.13695945589494826 chr11 135006516 2595561 0.019225449829399346 0.16307417246195707 chr12 133851895 2359808 0.017629993210032627 0.1448686539232483 chr13 115169878 1814013 0.015750759065664723 0.13688616576828916 chr14 107349540 1369340 0.012755900025281897 0.1238853768810729 chr15 102531392 1677152 0.016357448848446338 0.14087538828140586 chr16 90354753 1012942 0.011210721808956747 0.11731815003852321 chr17 81195210 1566468 0.019292615906775782 0.15316084531551788 chr18 78077248 2398713 0.03072230465909864 0.2307601836416793 chr19 59128983 1146732 0.019393737923752215 0.16795971990467445 chr20 63025520 1099181 0.017440252773797026 0.14504967628289223 chr21 48129895 573554 0.011916793086708375 0.12177389305178184 chr22 51304566 493948 0.009627759057546651 0.10653056559488536 chrMT 16571 61575 3.71582885764287 2.7715134969030015 chrX 155270560 4226011 0.027217078369524784 0.1836661148003719 chrY 59373566 119136 0.0020065495139705773 0.05344052068871735