BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063605.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 = 5,788,149 number of mapped reads = 5,437,434 (93.94%) number of supplementary alignments = 53,321 (0.92%) number of secondary alignments = 0 number of mapped bases = 346,855,526 bp number of sequenced bases = 346,726,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,199,687 duplication rate = 16.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2991 >>>>>>> ACTG content number of A's = 89,930,418 bp (25.94%) number of C's = 63,274,408 bp (18.25%) number of T's = 111,879,462 bp (32.27%) number of G's = 81,602,246 bp (23.54%) number of N's = 39,803 bp (0.01%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,836,479 number of insertions = 22,120 mapped reads with insertion percentage = 0.4% number of deletions = 75,078 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.112X std coverageData = 1.2438X There is a 6.09% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 29483732 0.11828950267690606 2.5248593803783352 chr2 243199373 36963333 0.1519877808237606 2.216716323737754 chr3 198022430 21151860 0.10681547539841825 0.5382597342967304 chr4 191154276 15539117 0.08129097253361992 0.5442454300746281 chr5 180915260 20039832 0.11076916341938209 0.5525207698277184 chr6 171115067 19699226 0.11512268525132273 0.8277250823209249 chr7 159138663 33131677 0.20819376244225452 1.8459764183785463 chr8 146364022 15422623 0.10537168075362127 1.2545575505033937 chr9 141213431 12903431 0.09137538057552047 0.7516213263146865 chr10 135534747 17001067 0.1254369626705394 0.7847333541839525 chr11 135006516 15076743 0.11167418763698783 0.7853802305810755 chr12 133851895 16235367 0.12129351624046862 0.5999525731880037 chr13 115169878 7738396 0.0671911452402511 0.5139485284311789 chr14 107349540 8585102 0.07997334688159818 0.5184666648105546 chr15 102531392 7594281 0.0740678620651127 0.515304094272113 chr16 90354753 7832817 0.08668959562094093 0.51581299739891 chr17 81195210 9258729 0.11403048283266956 0.6236819543899951 chr18 78077248 8518762 0.10910684249526828 1.5377082835239926 chr19 59128983 7723498 0.13062118792065136 1.6544631042674716 chr20 63025520 5380302 0.08536703862181541 0.5050489212277699 chr21 48129895 5678781 0.11798864302529644 0.5910559022935269 chr22 51304566 3924690 0.07649786960482231 0.44275095413502397 chrMT 16571 538139 32.47474503650957 21.19252197536613 chrX 155270560 20412737 0.13146559785705675 0.7054726130182235 chrY 59373566 1021284 0.017200988062600113 0.4880703960814317