BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234077.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 = 5,263,786 number of mapped reads = 4,965,413 (94.33%) number of supplementary alignments = 33,151 (0.63%) number of secondary alignments = 0 number of mapped bases = 320,051,619 bp number of sequenced bases = 319,933,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 521,028 duplication rate = 8.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8584 >>>>>>> ACTG content number of A's = 82,794,269 bp (25.88%) number of C's = 58,398,358 bp (18.25%) number of T's = 103,465,299 bp (32.34%) number of G's = 75,244,186 bp (23.52%) number of N's = 31,235 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,777,016 number of insertions = 20,392 mapped reads with insertion percentage = 0.41% number of deletions = 68,622 mapped reads with deletion percentage = 1.37% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.1034X std coverageData = 1.1839X There is a 7.88% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29819313 0.11963586241175303 2.7117673651259544 chr2 243199373 18626615 0.07658989729385528 1.9761761934531645 chr3 198022430 27597235 0.13936418717818985 0.46656958092943895 chr4 191154276 8749474 0.04577179325039007 0.3432696539913942 chr5 180915260 20451024 0.1130420065173054 0.44525618986418203 chr6 171115067 24923607 0.14565407615449785 0.7714421398090261 chr7 159138663 19557358 0.12289507547263986 1.3039477408676798 chr8 146364022 18936702 0.12938085289839876 1.2278026778307245 chr9 141213431 12425045 0.08798769998018106 0.7454896249850613 chr10 135534747 9581406 0.07069335511431618 0.6257585095570892 chr11 135006516 12837032 0.09508453651229694 0.7623728144066184 chr12 133851895 11272982 0.0842198162379397 0.3879097145199548 chr13 115169878 15995561 0.13888667139162897 0.5328619157764337 chr14 107349540 20076205 0.18701714977073958 0.6230354709812033 chr15 102531392 8697973 0.08483229214326866 0.436955955784231 chr16 90354753 8748696 0.09682607399745756 0.5366165307249394 chr17 81195210 7115307 0.08763210292823924 0.41623121165009824 chr18 78077248 6282989 0.08047144540750206 1.9976687065224883 chr19 59128983 11720236 0.19821474013852056 1.3501341279100154 chr20 63025520 9268192 0.14705458995022969 0.5526261736726368 chr21 48129895 7422442 0.1542168749796774 0.5304296675892557 chr22 51304566 4378331 0.0853399870880888 0.3574759224045083 chrMT 16571 210286 12.690000603463883 8.073806291113451 chrX 155270560 4716297 0.030374702068441048 0.4179286013086157 chrY 59373566 641311 0.010801288236586631 0.22626103367341077