BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867871.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,100,975 number of mapped reads = 1,936,607 (92.18%) number of supplementary alignments = 8,857 (0.42%) number of secondary alignments = 0 number of mapped bases = 114,742,166 bp number of sequenced bases = 114,707,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,632 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9091 >>>>>>> ACTG content number of A's = 29,736,103 bp (25.92%) number of C's = 23,563,414 bp (20.54%) number of T's = 34,659,892 bp (30.22%) number of G's = 26,732,218 bp (23.3%) number of N's = 15,754 bp (0.01%) GC percentage = 43.85% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 571,601 number of insertions = 6,938 mapped reads with insertion percentage = 0.36% number of deletions = 21,501 mapped reads with deletion percentage = 1.1% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.0371X std coverageData = 0.3481X There is a 3.27% of reference with a coverageData >= 1X There is a 0.31% 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 0.01% 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 9218397 0.036984449479064686 0.6551543901901096 chr2 243199373 9754047 0.04010720455270253 0.4730065783394899 chr3 198022430 7552241 0.03813831089740693 0.21616961590985467 chr4 191154276 7407022 0.03874892131630893 0.2564620658817719 chr5 180915260 6960127 0.038471751913022705 0.21956103068506597 chr6 171115067 6589624 0.03850989930652921 0.2496551678101595 chr7 159138663 6274894 0.03943035514883018 0.40786472742761837 chr8 146364022 5817697 0.03974813564497428 0.3875506552855678 chr9 141213431 4858381 0.034404524878373643 0.2814191964944933 chr10 135534747 5540470 0.04087859477097781 0.3502326928303498 chr11 135006516 5251415 0.03889749291804553 0.2995890693562428 chr12 133851895 5167804 0.0386083738298961 0.2201466281340473 chr13 115169878 3571080 0.031007065927429394 0.1970928915203774 chr14 107349540 3422964 0.031886154332845765 0.20320761977349777 chr15 102531392 3307908 0.032262392380277054 0.1999668401332642 chr16 90354753 3399789 0.037627118520262015 0.23561474265389432 chr17 81195210 3129877 0.0385475571773261 0.23344235214896286 chr18 78077248 3046958 0.039024915427347026 0.5138987555856611 chr19 59128983 2433942 0.041163265060723264 0.4829426417225096 chr20 63025520 2459125 0.03901792480252444 0.2251363992314664 chr21 48129895 1513357 0.03144318100008321 0.23284628175609706 chr22 51304566 1382701 0.026950837085338564 0.1820213957965254 chrMT 16571 9912 0.5981534005189789 0.8513675557521443 chrX 155270560 6282783 0.04046345295592416 0.24624708648326565 chrY 59373566 389651 0.006562701657501926 0.24860256058487182