BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472609.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,115,858 number of mapped reads = 18,002,052 (99.37%) number of supplementary alignments = 78,944 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,023,120 number of mapped paired reads (second in pair) = 8,978,932 number of mapped paired reads (both in pair) = 17,926,976 number of mapped paired reads (singletons) = 75,076 number of mapped bases = 1,770,932,916 bp number of sequenced bases = 1,770,719,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,474,635 duplication rate = 50.88% >>>>>>> Insert size mean insert size = 19,192.0243 std insert size = 1,407,592.8986 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 54.71 >>>>>>> ACTG content number of A's = 468,015,901 bp (26.43%) number of C's = 419,234,646 bp (23.68%) number of T's = 469,875,404 bp (26.54%) number of G's = 413,261,703 bp (23.34%) number of N's = 331,603 bp (0.02%) GC percentage = 47.01% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,917,256 number of insertions = 99,768 mapped reads with insertion percentage = 0.55% number of deletions = 91,783 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.5% >>>>>>> Coverage mean coverageData = 0.5721X std coverageData = 23.8111X There is a 3.5% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 315455794 1.2656168828562318 42.33829029344035 chr2 243199373 98462132 0.4048617839158656 16.357110081770667 chr3 198022430 120119776 0.6065968183503253 18.652349702999587 chr4 191154276 27131635 0.141935799542355 6.60242476767621 chr5 180915260 71995975 0.39795413056919576 21.03036309910741 chr6 171115067 155515991 0.9088386763744188 35.296635048690035 chr7 159138663 80796655 0.5077122898789215 17.405014838201463 chr8 146364022 87420358 0.5972803753643775 19.736980946987263 chr9 141213431 81080277 0.5741683098118336 16.43360821415519 chr10 135534747 37618746 0.2775579460815314 11.699456963828945 chr11 135006516 44409322 0.3289420638037945 11.634566921531643 chr12 133851895 72360643 0.5406023052568661 17.623596449509723 chr13 115169878 68064655 0.5909935495460019 25.779917114233903 chr14 107349540 32132860 0.29932927518832403 12.685965294995086 chr15 102531392 22095860 0.21550336505721096 8.752544822949172 chr16 90354753 104515114 1.1567196027861424 40.548488164244404 chr17 81195210 82788705 1.019625480370086 28.467634215581747 chr18 78077248 17487175 0.2239727378710889 11.371581772478763 chr19 59128983 68003556 1.150088375441871 46.24723433072672 chr20 63025520 64077605 1.016692999914955 26.696372938042987 chr21 48129895 10045627 0.20871907158741984 10.296461127797782 chr22 51304566 19876426 0.3874202151909832 11.529278133517925 chrMT 16571 810 0.04888057449761632 0.2227762916568317 chrX 155270560 86990924 0.560253817594269 30.036776383446007 chrY 59373566 2486295 0.04187545346358344 4.5804920164115215