BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231831.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 = 8,942,502 number of mapped reads = 4,115,522 (46.02%) number of supplementary alignments = 34,620 (0.39%) number of secondary alignments = 0 number of mapped bases = 253,092,812 bp number of sequenced bases = 253,007,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 693,297 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2985 >>>>>>> ACTG content number of A's = 74,977,781 bp (29.63%) number of C's = 50,343,866 bp (19.9%) number of T's = 72,410,591 bp (28.62%) number of G's = 55,256,296 bp (21.84%) number of N's = 18,950 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,422,809 number of insertions = 17,172 mapped reads with insertion percentage = 0.41% number of deletions = 50,488 mapped reads with deletion percentage = 1.21% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0818X std coverageData = 7.1833X There is a 3.54% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 16047837 0.06438434109257445 1.2784520953571712 chr2 243199373 34132552 0.14034802630843954 25.499898211574475 chr3 198022430 18340002 0.09261578094966312 0.5963718146865317 chr4 191154276 18428785 0.09640791399298858 0.6294545579021408 chr5 180915260 14530493 0.08031656920483103 0.5524044895985527 chr6 171115067 14068117 0.08221436748173672 0.6196352049814715 chr7 159138663 12542868 0.07881722620731078 0.855741520653664 chr8 146364022 14346618 0.09802011316688196 0.8499085840216513 chr9 141213431 11060636 0.07832566577891589 0.7334681657717217 chr10 135534747 9221492 0.0680378441994657 0.7079972648378356 chr11 135006516 10124901 0.07499564687677741 0.6420018296088671 chr12 133851895 10317787 0.07708360796834442 0.5550747378394272 chr13 115169878 7249966 0.06295019258421025 0.4889984499667707 chr14 107349540 6237827 0.05810762673039866 0.5536853161187688 chr15 102531392 12184137 0.1188332349959708 0.6717658302967512 chr16 90354753 6103314 0.06754834468973647 0.5480798350906815 chr17 81195210 5640577 0.06946933199630866 0.5720658525812062 chr18 78077248 5330886 0.06827707349521335 1.3393645178796403 chr19 59128983 4242072 0.07174268497058371 0.9883919274874138 chr20 63025520 3460164 0.0549009988334884 0.45899152184652664 chr21 48129895 2990832 0.06214083783062481 0.5165595106764217 chr22 51304566 2668172 0.05200652121294623 0.4340615006191173 chrMT 16571 27254 1.6446804658741174 2.5532447829130653 chrX 155270560 13201403 0.08502193203914508 0.6360218425970386 chrY 59373566 594120 0.010006473251076077 0.25909688940506226