BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008723.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 = 1,768,083 number of mapped reads = 1,275,770 (72.16%) number of supplementary alignments = 4,858 (0.27%) number of secondary alignments = 0 number of mapped bases = 81,930,461 bp number of sequenced bases = 81,888,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,509 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3193 >>>>>>> ACTG content number of A's = 23,307,601 bp (28.46%) number of C's = 13,734,893 bp (16.77%) number of T's = 25,498,655 bp (31.14%) number of G's = 19,337,888 bp (23.61%) number of N's = 9,838 bp (0.01%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 767,064 number of insertions = 6,560 mapped reads with insertion percentage = 0.51% number of deletions = 26,341 mapped reads with deletion percentage = 2.04% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2354X There is a 2.3% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 7224967 0.02898675626569452 0.3203540978088669 chr2 243199373 7032971 0.028918540838507836 0.32933070717043356 chr3 198022430 6441968 0.03253150665810939 0.20385499586694864 chr4 191154276 5238115 0.027402552062188765 0.1888029809958181 chr5 180915260 3242099 0.017920539151865908 0.15044361990947874 chr6 171115067 5807962 0.033941850369026826 0.2331553328455918 chr7 159138663 3168091 0.019907739202257843 0.23731463240304135 chr8 146364022 6356401 0.043428712282858696 0.3374538962573579 chr9 141213431 2254261 0.01596350279174224 0.20538224389355755 chr10 135534747 4818695 0.03555320762136369 0.2512412437554634 chr11 135006516 2425873 0.017968562347020347 0.19329178906459193 chr12 133851895 3233574 0.024157849987854113 0.17595753667380712 chr13 115169878 3126493 0.02714679440747519 0.18565263343877497 chr14 107349540 3117496 0.0290406088372619 0.1951192887161162 chr15 102531392 2374356 0.02315735652940321 0.17203211842526397 chr16 90354753 2131968 0.023595526845167736 0.18027579504606733 chr17 81195210 1474015 0.018153964993747784 0.1589657506923434 chr18 78077248 2187677 0.028019391769545977 0.3598563305767903 chr19 59128983 1380411 0.023345759219298597 0.2296150827915679 chr20 63025520 2088995 0.03314522434721681 0.2096198056255116 chr21 48129895 799279 0.016606705665989922 0.14922729295522558 chr22 51304566 957587 0.018664751983283514 0.15263194040046613 chrMT 16571 26011 1.5696699052561705 1.7640688379004807 chrX 155270560 4828878 0.031099765467452425 0.20998439913023773 chrY 59373566 192318 0.0032391182298196473 0.0803794606318023