BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238059.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 = 1,730,913 number of mapped reads = 1,561,084 (90.19%) number of supplementary alignments = 15,450 (0.89%) number of secondary alignments = 0 number of mapped bases = 104,978,901 bp number of sequenced bases = 104,930,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,270 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9547 >>>>>>> ACTG content number of A's = 28,846,932 bp (27.49%) number of C's = 20,101,661 bp (19.16%) number of T's = 32,545,814 bp (31.02%) number of G's = 23,430,158 bp (22.33%) number of N's = 5,782 bp (0.01%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 757,707 number of insertions = 7,228 mapped reads with insertion percentage = 0.46% number of deletions = 27,484 mapped reads with deletion percentage = 1.74% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.3124X There is a 2.84% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8010172 0.03213701922933223 0.5375584749724042 chr2 243199373 4614346 0.018973511087135905 0.31792693194247473 chr3 198022430 13126403 0.06628745541603545 0.30042907253059536 chr4 191154276 11708282 0.061250432085547486 0.29240069270742797 chr5 180915260 9266128 0.05121805645361259 0.2616600306296169 chr6 171115067 6096177 0.035626184805806725 0.24131180359933166 chr7 159138663 6491389 0.040790772510134764 0.47130203978974655 chr8 146364022 4854824 0.03316951757447605 0.4288694073741592 chr9 141213431 3347999 0.02370878588737073 0.24482409289768822 chr10 135534747 4829889 0.03563579898813697 0.3178942706209306 chr11 135006516 1279624 0.009478238813302908 0.1482029461905001 chr12 133851895 4626123 0.034561505460942485 0.21818957104765135 chr13 115169878 5560908 0.04828439602931593 0.25460153650199724 chr14 107349540 1058766 0.009862790283032418 0.14195695815071172 chr15 102531392 874658 0.008530636158728832 0.1065745561714308 chr16 90354753 2511461 0.027795560461550926 0.20450557119083282 chr17 81195210 1015109 0.012502079864070799 0.13084602910121534 chr18 78077248 3910998 0.05009139154084939 0.4182639588527423 chr19 59128983 2181829 0.036899484640214426 0.40722669925853544 chr20 63025520 2272191 0.03605191992069244 0.2261879990330335 chr21 48129895 1019859 0.02118972002743825 0.1834469499904381 chr22 51304566 1147455 0.022365553194622093 0.17227910983200645 chrMT 16571 54563 3.292679983103011 2.6607386252776095 chrX 155270560 4905634 0.03159410257810624 0.22236262555497902 chrY 59373566 214114 0.0036062176221653927 0.0936064161184728