BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548929.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,872,336 number of mapped reads = 9,472,293 (87.12%) number of secondary alignments = 0 number of mapped bases = 374,676,872 bp number of sequenced bases = 374,636,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 392,148 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6527 >>>>>>> ACTG content number of A's = 110,844,830 bp (29.59%) number of C's = 76,215,753 bp (20.34%) number of T's = 111,519,809 bp (29.77%) number of G's = 76,053,115 bp (20.3%) number of N's = 3,308 bp (0%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,110,533 number of insertions = 13,003 mapped reads with insertion percentage = 0.14% number of deletions = 30,722 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 0.121X std coverageData = 1.3209X There is a 9.56% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% 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 29127763 0.11686134575367818 1.4025999035361016 chr2 243199373 31754728 0.13057076425933056 0.7824779315353902 chr3 198022430 25613742 0.12934768046225875 0.43824441286999616 chr4 191154276 25312345 0.1324184084691885 0.4618204880840365 chr5 180915260 23699476 0.13099766155712902 0.4511537911176208 chr6 171115067 22054079 0.1288844950164441 0.5083131129893401 chr7 159138663 21036249 0.132188172273384 1.2308735967318927 chr8 146364022 19732601 0.1348186578256233 4.970058895306197 chr9 141213431 15675680 0.1110070047090634 0.7763907148101599 chr10 135534747 17270792 0.1274270427494139 0.6675074991044668 chr11 135006516 16851710 0.12482145676583492 0.8470815456984749 chr12 133851895 16999061 0.1269990312800577 0.46520841534898627 chr13 115169878 12302944 0.10682432085236732 0.3875064436684783 chr14 107349540 11516584 0.10728116766965187 0.5300647776381935 chr15 102531392 10498564 0.10239365520366679 0.38861987476641596 chr16 90354753 9916748 0.10975347362191339 0.4798880793353268 chr17 81195210 9295184 0.11447946252001812 0.47240941342560316 chr18 78077248 9987807 0.12792211887386196 1.4908075887350245 chr19 59128983 6952836 0.11758761350588424 1.332125152824277 chr20 63025520 7206388 0.1143407940148689 0.4358736010383292 chr21 48129895 4755386 0.09880316589097067 0.45766119295677654 chr22 51304566 3793746 0.0739455821534481 0.39232225824822964 chrMT 16571 9413 0.5680405527729165 0.9212699436637091 chrX 155270560 22132275 0.14254006039522238 0.6182508686749717 chrY 59373566 1180771 0.019887149779752155 0.2476940394481502