BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695977.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 13,668,259 number of mapped reads = 12,472,495 (91.25%) number of supplementary alignments = 19,477 (0.14%) number of secondary alignments = 0 number of mapped bases = 1,713,182,631 bp number of sequenced bases = 1,701,203,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,788,607 duplication rate = 18.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.0169 >>>>>>> ACTG content number of A's = 470,313,075 bp (27.65%) number of C's = 378,614,490 bp (22.26%) number of T's = 468,747,647 bp (27.55%) number of G's = 383,528,567 bp (22.54%) number of N's = 0 bp (0%) GC percentage = 44.8% >>>>>>> Mismatches and indels general error rate = 0.0203 number of mismatches = 23,948,653 number of insertions = 9,780,546 mapped reads with insertion percentage = 47.11% number of deletions = 10,771,435 mapped reads with deletion percentage = 51.65% homopolymer indels = 36.69% >>>>>>> Coverage mean coverageData = 0.5534X std coverageData = 1.867X There is a 18.88% of reference with a coverageData >= 1X There is a 10.92% of reference with a coverageData >= 2X There is a 6.88% of reference with a coverageData >= 3X There is a 4.6% of reference with a coverageData >= 4X There is a 3.21% of reference with a coverageData >= 5X There is a 2.31% of reference with a coverageData >= 6X There is a 1.7% of reference with a coverageData >= 7X There is a 1.28% of reference with a coverageData >= 8X There is a 0.98% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 196488497 0.7883169807629085 2.551814734772041 chr2 243199373 136320636 0.5605303760384284 1.9498067768437308 chr3 198022430 117461898 0.593174712581802 1.7859909295494119 chr4 191154276 59524418 0.3113946454433486 1.2523186632098486 chr5 180915260 141145258 0.7801733142909006 2.323584147170524 chr6 171115067 82062943 0.4795775406498833 1.5502157158206933 chr7 159138663 92244968 0.5796515206364402 1.7597477571570574 chr8 146364022 76079160 0.5197941335610469 1.6745664833835758 chr9 141213431 72259951 0.5117073531058105 1.78819272346309 chr10 135534747 77749408 0.5736492650109865 1.7845817817317498 chr11 135006516 97730289 0.7238931267584151 2.1059414858776835 chr12 133851895 83272326 0.6221228769305059 1.863025519902574 chr13 115169878 32986550 0.2864164708067156 1.106613338861514 chr14 107349540 37777445 0.35191063697152314 1.2872859109583155 chr15 102531392 65902132 0.6427507782201962 2.0164002434395467 chr16 90354753 70605256 0.7814227105462842 2.3328181380512247 chr17 81195210 49067970 0.6043209938123197 1.866563824505207 chr18 78077248 32553208 0.41693590429826627 1.637643129700997 chr19 59128983 23982439 0.4055953237010689 1.591126358380503 chr20 63025520 60646673 0.9622558132007479 2.6740585008300917 chr21 48129895 15133270 0.31442557686859696 2.001078995126071 chr22 51304566 20196451 0.3936579640884205 1.419439322092953 chrMT 16571 207039 12.494055880755537 13.297951776306071 chrX 155270560 69929667 0.450372994082072 1.4710860434307875 chrY 59373566 1854779 0.031239137632393513 0.6281405057604226