BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524435.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 = 1,359,641 number of mapped reads = 1,259,640 (92.65%) number of supplementary alignments = 5,540 (0.41%) number of secondary alignments = 0 number of mapped bases = 73,882,408 bp number of sequenced bases = 73,861,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,555 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7878 >>>>>>> ACTG content number of A's = 17,337,769 bp (23.47%) number of C's = 13,640,681 bp (18.47%) number of T's = 23,976,008 bp (32.46%) number of G's = 18,899,613 bp (25.59%) number of N's = 7,764 bp (0.01%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 370,799 number of insertions = 5,231 mapped reads with insertion percentage = 0.41% number of deletions = 12,869 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.19% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2484X There is a 2.13% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% 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 5972599 0.02396222314727954 0.45086304438128133 chr2 243199373 6281228 0.025827484349640984 0.31868176067405896 chr3 198022430 4863562 0.024560662143172367 0.17166433352406643 chr4 191154276 4692674 0.024549144796530736 0.2063695308415231 chr5 180915260 4290281 0.023714312435556845 0.1673893021908542 chr6 171115067 4162838 0.024327711597716874 0.1844436448757889 chr7 159138663 4059826 0.025511248639810427 0.33221495400589657 chr8 146364022 3703939 0.025306348851222467 0.20582102211769387 chr9 141213431 3056819 0.02164680072110138 0.19755007495981425 chr10 135534747 3593315 0.02651213123967391 0.25450909112722797 chr11 135006516 3325166 0.024629670467164713 0.22342750692216365 chr12 133851895 3371351 0.025187174227156068 0.1765701077925679 chr13 115169878 2251348 0.019548062732166825 0.152526351699096 chr14 107349540 2260309 0.02105560023824974 0.1656651950454206 chr15 102531392 2204910 0.021504730960835876 0.159908456862515 chr16 90354753 2237944 0.02476841478389078 0.18443802164373269 chr17 81195210 2093470 0.02578317119938479 0.18850212308218486 chr18 78077248 1924417 0.02464760284583801 0.3481309017405481 chr19 59128983 1642953 0.02778591676437256 0.3268966178617993 chr20 63025520 1649176 0.026166797195802588 0.18379954408528865 chr21 48129895 981193 0.020386352390754228 0.17907397754014692 chr22 51304566 932019 0.01816639478053474 0.14939203795398392 chrMT 16571 2706 0.16329732665499969 0.4496303897893214 chrX 155270560 4064296 0.026175573785526374 0.19271632737983038 chrY 59373566 264069 0.004447585310944605 0.14616687357589617