BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238288.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 = 2,412,999 number of mapped reads = 2,122,119 (87.95%) number of supplementary alignments = 24,632 (1.02%) number of secondary alignments = 0 number of mapped bases = 140,045,658 bp number of sequenced bases = 139,978,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,756 duplication rate = 5.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8273 >>>>>>> ACTG content number of A's = 38,774,607 bp (27.7%) number of C's = 26,962,471 bp (19.26%) number of T's = 42,963,121 bp (30.69%) number of G's = 31,249,019 bp (22.32%) number of N's = 28,965 bp (0.02%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,229,951 number of insertions = 11,193 mapped reads with insertion percentage = 0.52% number of deletions = 40,774 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.38X There is a 3.31% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11185207 0.04487534255732105 0.613747725218148 chr2 243199373 11160107 0.045888716168688476 0.43546513835071216 chr3 198022430 9786894 0.049423158780548246 0.29165171087814384 chr4 191154276 8288093 0.04335813549888887 0.28312999631357316 chr5 180915260 9315892 0.051493124460590005 0.29595390005132804 chr6 171115067 9210844 0.053828363343363564 0.3524013294840625 chr7 159138663 7075922 0.04446387739225885 0.42078450920180455 chr8 146364022 6901977 0.047156240349831326 0.4164318977046326 chr9 141213431 5219351 0.03696072649066929 0.3459967460651198 chr10 135534747 7383520 0.05447695268874483 0.421904038531905 chr11 135006516 5961716 0.04415872786466099 0.347905808589183 chr12 133851895 7767229 0.05802853220718317 0.3194218240825296 chr13 115169878 4703699 0.040841399519412534 0.26324919510845757 chr14 107349540 4159229 0.03874473053168183 0.2800554012624841 chr15 102531392 3931638 0.038345700017415156 0.2625324508322038 chr16 90354753 3803335 0.04209335838702365 0.28932986565912805 chr17 81195210 3214146 0.039585413967153975 0.28622555420217727 chr18 78077248 3599033 0.046095797331381354 0.6448097402786607 chr19 59128983 2770320 0.046852150323640776 0.4916955799694668 chr20 63025520 2840920 0.045075709014380204 0.2854875897865144 chr21 48129895 1584306 0.032917295996594216 0.2491650997689471 chr22 51304566 1476365 0.028776483558987712 0.21818831462552832 chrMT 16571 9921 0.5986965180133969 0.9494533559004718 chrX 155270560 8326280 0.053624331618305494 0.3279308604900628 chrY 59373566 369714 0.00622691249503188 0.14390679831631029