BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013357.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,438,245 number of mapped reads = 1,247,972 (86.77%) number of supplementary alignments = 7,384 (0.51%) number of secondary alignments = 0 number of mapped bases = 80,050,175 bp number of sequenced bases = 80,004,851 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,369 duplication rate = 9.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8112 >>>>>>> ACTG content number of A's = 21,346,926 bp (26.68%) number of C's = 14,385,369 bp (17.98%) number of T's = 25,825,614 bp (32.28%) number of G's = 18,445,825 bp (23.06%) number of N's = 1,117 bp (0%) GC percentage = 41.04% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 644,343 number of insertions = 5,784 mapped reads with insertion percentage = 0.46% number of deletions = 25,183 mapped reads with deletion percentage = 1.99% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.2795X There is a 1.72% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.18% 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% 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 6001823 0.024079470598390204 0.3313015938046331 chr2 243199373 6672349 0.02743571629191659 0.33719207025405246 chr3 198022430 5841363 0.029498491660767925 0.24170984372176807 chr4 191154276 4946939 0.025879300759141795 0.23741749052184574 chr5 180915260 4195567 0.023190785564468137 0.21186972151749237 chr6 171115067 6861035 0.04009603081884075 0.30910328880998006 chr7 159138663 4788596 0.030090714033458983 0.4642381746549181 chr8 146364022 5190111 0.035460292284124305 0.3383428461893535 chr9 141213431 3307065 0.023418912610373443 0.2574196231644163 chr10 135534747 3666430 0.02705158700004804 0.27872710698624037 chr11 135006516 2967895 0.021983346344557175 0.2337060311657081 chr12 133851895 3391052 0.02533435929315756 0.22592479205492624 chr13 115169878 2137422 0.018558863108286004 0.18979187995199634 chr14 107349540 2597357 0.024195324917088607 0.22386539439535735 chr15 102531392 1653032 0.016122203822220613 0.18143144249254325 chr16 90354753 1962190 0.021716511139153908 0.2105717986275266 chr17 81195210 2084282 0.02567001181473636 0.2309820729716587 chr18 78077248 2213208 0.028346388438281023 0.39140921934310263 chr19 59128983 1518432 0.025679995206411718 0.28234368834320667 chr20 63025520 1466757 0.0232724299617044 0.21504387089239843 chr21 48129895 1492937 0.031018912465942426 0.25469507496692306 chr22 51304566 736361 0.014352738116915363 0.16537731543862028 chrMT 16571 31011 1.871401846599481 2.0825972500434107 chrX 155270560 4151184 0.026735164734383646 0.23593031006068155 chrY 59373566 175777 0.0029605262382252735 0.09616850677669851