BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083627.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,371,359 number of mapped reads = 1,267,562 (92.43%) number of supplementary alignments = 11,540 (0.84%) number of secondary alignments = 0 number of mapped bases = 84,836,381 bp number of sequenced bases = 84,804,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,686 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.771 >>>>>>> ACTG content number of A's = 23,111,162 bp (27.25%) number of C's = 15,676,591 bp (18.49%) number of T's = 26,845,717 bp (31.66%) number of G's = 19,166,661 bp (22.6%) number of N's = 4,667 bp (0.01%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 593,371 number of insertions = 6,650 mapped reads with insertion percentage = 0.52% number of deletions = 19,595 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.287X There is a 2.38% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 9361410 0.037558221369486576 0.6064378233200972 chr2 243199373 7392164 0.030395489547582016 0.34227810028447636 chr3 198022430 6545882 0.03305626539377383 0.20479808413960354 chr4 191154276 2823180 0.014769117694233532 0.14260516163148118 chr5 180915260 4032675 0.022290408227586773 0.16731482413750978 chr6 171115067 4959089 0.02898101895375467 0.22058930303013213 chr7 159138663 6673472 0.04193495077937157 0.4108936531113261 chr8 146364022 5287819 0.03612786071156203 0.26976595011201737 chr9 141213431 3711452 0.02628257081297033 0.2216675080881891 chr10 135534747 3569875 0.026339186658901573 0.23490641655735955 chr11 135006516 3299325 0.024438264890859044 0.20848908026618215 chr12 133851895 3949786 0.029508629668634875 0.19202312277185957 chr13 115169878 2592178 0.022507430284852782 0.1682606586420232 chr14 107349540 1142152 0.01063956119420726 0.11931302865641251 chr15 102531392 2314872 0.02257720250203957 0.17390006438563083 chr16 90354753 2717334 0.030074057089171612 0.20278886460588313 chr17 81195210 1768732 0.02178369881671591 0.16993489906944692 chr18 78077248 2353900 0.030148347441754094 0.38809459077324354 chr19 59128983 2593688 0.04386491815697219 0.41806813486952615 chr20 63025520 2074160 0.032909843504662875 0.2059329436575557 chr21 48129895 1408763 0.029270020223397537 0.19381581972253456 chr22 51304566 814356 0.015872973177475082 0.1387306733100854 chrMT 16571 2527 0.15249532315490918 0.4616059336272891 chrX 155270560 3272075 0.021073376691627826 0.16925989793952884 chrY 59373566 175515 0.002956113500071732 0.0720040187199421