BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975333.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 = 3,576,714 number of mapped reads = 3,513,725 (98.24%) number of supplementary alignments = 18,729 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,755,458 number of mapped paired reads (second in pair) = 1,758,267 number of mapped paired reads (both in pair) = 3,495,864 number of mapped paired reads (singletons) = 17,861 number of mapped bases = 318,681,732 bp number of sequenced bases = 318,489,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 240,998 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 73,255.2456 std insert size = 2,507,144.7336 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.6524 >>>>>>> ACTG content number of A's = 93,929,393 bp (29.49%) number of C's = 60,017,230 bp (18.84%) number of T's = 96,135,283 bp (30.18%) number of G's = 68,400,731 bp (21.48%) number of N's = 6,898 bp (0%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 2,502,497 number of insertions = 52,182 mapped reads with insertion percentage = 1.44% number of deletions = 104,454 mapped reads with deletion percentage = 2.91% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.1029X std coverageData = 1.3864X There is a 6.88% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 0.01% 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 23073751 0.09257249152450457 1.1375932139918739 chr2 243199373 29567477 0.12157711031598753 1.662644582370201 chr3 198022430 21796051 0.1100685967746179 0.4622371743397679 chr4 191154276 20603972 0.10778713629194463 1.0833787857050954 chr5 180915260 19648139 0.10860410006320086 0.4405427453446446 chr6 171115067 18380823 0.10741791077930034 1.1529284710390335 chr7 159138663 18119673 0.11386091009197431 1.8068093998243342 chr8 146364022 17241807 0.11780085545886407 0.6844174964053512 chr9 141213431 13962420 0.09887458934412549 1.7205449469323426 chr10 135534747 17093472 0.12611874355732555 3.444466131310555 chr11 135006516 14880105 0.11021768015997095 0.8829451387710517 chr12 133851895 14168585 0.10585270384106255 0.4283732043430478 chr13 115169878 9849558 0.0855219973403115 0.3770251977044151 chr14 107349540 9873471 0.0919749725988579 0.44411526410663993 chr15 102531392 8925223 0.08704868651349237 0.3884824061236836 chr16 90354753 11679719 0.129265131187952 2.9097920642328567 chr17 81195210 7260895 0.08942516436622308 1.351332227207014 chr18 78077248 9756515 0.12495977061076743 1.9857468615974931 chr19 59128983 3958714 0.06695048348793688 0.7092456454004485 chr20 63025520 6337597 0.10055604459907669 0.49250465619837297 chr21 48129895 4238052 0.08805446178513375 0.5644030801775864 chr22 51304566 2832841 0.05521615756383165 0.3409695060296163 chrMT 16571 74302 4.483857341138133 3.886368582982578 chrX 155270560 10138214 0.0652938586683786 0.5007452692172241 chrY 59373566 5220356 0.08792390876438178 2.2535644046628125