BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975337.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,534,996 number of mapped reads = 4,364,044 (96.23%) number of supplementary alignments = 25,072 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,179,998 number of mapped paired reads (second in pair) = 2,184,046 number of mapped paired reads (both in pair) = 4,320,494 number of mapped paired reads (singletons) = 43,550 number of mapped bases = 394,434,186 bp number of sequenced bases = 394,186,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 289,559 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 74,974.5083 std insert size = 2,577,116.9481 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.6027 >>>>>>> ACTG content number of A's = 118,932,135 bp (30.17%) number of C's = 73,852,818 bp (18.74%) number of T's = 119,298,932 bp (30.26%) number of G's = 82,094,415 bp (20.83%) number of N's = 7,999 bp (0%) GC percentage = 39.56% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,976,030 number of insertions = 75,467 mapped reads with insertion percentage = 1.68% number of deletions = 134,053 mapped reads with deletion percentage = 3% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.1274X std coverageData = 1.574X There is a 8.48% of reference with a coverageData >= 1X There is a 2.58% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 29062967 0.11660138250969493 1.671582844733326 chr2 243199373 34815405 0.14315581726438087 1.9768171443422313 chr3 198022430 22870851 0.11549626474132249 0.4725022926618777 chr4 191154276 27068201 0.14160395240125312 1.792340532319215 chr5 180915260 23940646 0.13233071660179468 0.5772077001214378 chr6 171115067 34073425 0.1991258022883514 2.1535288255608123 chr7 159138663 20352286 0.12789026636474884 1.4921192001603272 chr8 146364022 28281543 0.19322742442811527 0.8523774307679933 chr9 141213431 16248074 0.11506040101808729 2.706093614606868 chr10 135534747 19847368 0.1464374888308162 3.081463514080102 chr11 135006516 17216006 0.12751981541394639 1.0473651446975702 chr12 133851895 16381304 0.12238380338208883 0.4673801445146649 chr13 115169878 12215995 0.1060693578228849 0.42449584191223544 chr14 107349540 11283603 0.10511086493710173 0.5167851405297872 chr15 102531392 9896729 0.09652389192180284 0.4035610527873737 chr16 90354753 10992117 0.12165510540436096 1.6508097185870512 chr17 81195210 7479721 0.09212022482607041 1.5878379270289154 chr18 78077248 15745483 0.20166544548291457 2.582635630592879 chr19 59128983 4271181 0.07223498161637584 1.0123219483808306 chr20 63025520 7026705 0.11148983776730442 0.5427210254042454 chr21 48129895 4859244 0.10096103471657272 0.6337149257158404 chr22 51304566 3057928 0.05960342788982953 0.386561354299378 chrMT 16571 113336 6.83941826081709 5.073177739298795 chrX 155270560 12153424 0.07827255855842859 0.5621682986894568 chrY 59373566 5180644 0.08725505892639158 2.441614215378621