BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617406.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,002,939 (93.76%) number of supplementary alignments = 487,175 (1.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,144,166 number of mapped paired reads (second in pair) = 14,858,773 number of mapped paired reads (both in pair) = 29,394,788 number of mapped paired reads (singletons) = 608,151 number of mapped bases = 2,951,863,180 bp number of sequenced bases = 2,951,214,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,406,478 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 57,498.2093 std insert size = 2,286,240.8641 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 53.8798 >>>>>>> ACTG content number of A's = 880,977,866 bp (29.85%) number of C's = 592,830,528 bp (20.09%) number of T's = 872,701,998 bp (29.57%) number of G's = 603,821,152 bp (20.46%) number of N's = 882,638 bp (0.03%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 27,715,072 number of insertions = 252,352 mapped reads with insertion percentage = 0.83% number of deletions = 287,319 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.9535X std coverageData = 2.9292X There is a 29.56% of reference with a coverageData >= 1X There is a 16.98% of reference with a coverageData >= 2X There is a 10.87% of reference with a coverageData >= 3X There is a 7.53% of reference with a coverageData >= 4X There is a 5.47% of reference with a coverageData >= 5X There is a 4.12% of reference with a coverageData >= 6X There is a 3.19% of reference with a coverageData >= 7X There is a 2.52% of reference with a coverageData >= 8X There is a 2.03% of reference with a coverageData >= 9X There is a 1.66% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.15% of reference with a coverageData >= 12X There is a 0.97% of reference with a coverageData >= 13X There is a 0.83% of reference with a coverageData >= 14X There is a 0.71% of reference with a coverageData >= 15X There is a 0.62% of reference with a coverageData >= 16X There is a 0.54% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190389513 0.7638476976954052 2.7363193321966803 chr2 243199373 294594120 1.2113276295329922 3.1146209001855762 chr3 198022430 249126338 1.258071310406604 3.419767934147929 chr4 191154276 141618920 0.7408618994220145 2.2751112493923964 chr5 180915260 189130033 1.0454067445720168 2.86860499564954 chr6 171115067 135000899 0.7889480533002976 2.591208522983285 chr7 159138663 221009463 1.3887854706935674 3.236471773922684 chr8 146364022 130531491 0.8918277129607712 3.2629434918633646 chr9 141213431 118045684 0.8359380773065418 2.617612514021392 chr10 135534747 94636528 0.6982455060029735 2.421513197260502 chr11 135006516 218957929 1.6218323047459429 3.8275108180249098 chr12 133851895 140491483 1.0496039895438163 2.805247715423554 chr13 115169878 127830984 1.1099341791436126 2.762553187440578 chr14 107349540 85886913 0.8000678251625485 2.897901749787887 chr15 102531392 67500443 0.6583392820805554 2.3673472229404244 chr16 90354753 74446027 0.823930391354177 3.3103219209080175 chr17 81195210 91211849 1.1233649004664192 3.7135702584592596 chr18 78077248 42094059 0.5391334873893097 1.9988465887402285 chr19 59128983 42111088 0.7121902976075202 2.3375583770285657 chr20 63025520 101018799 1.602823729181449 4.7342089674332595 chr21 48129895 40452593 0.8404878714154685 2.5085229131312143 chr22 51304566 23834155 0.46456206256573734 2.0806169200497404 chrMT 16571 183639 11.081950395268843 5.29442044236192 chrX 155270560 129384059 0.8332813316317015 2.56969187729135 chrY 59373566 2376171 0.04002068866808505 0.6140851498893567