BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975276.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 = 3,229,748 number of mapped reads = 3,188,263 (98.72%) number of supplementary alignments = 15,479 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,593,695 number of mapped paired reads (second in pair) = 1,594,568 number of mapped paired reads (both in pair) = 3,177,858 number of mapped paired reads (singletons) = 10,405 number of mapped bases = 290,234,880 bp number of sequenced bases = 290,068,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,251 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 51,230.884 std insert size = 2,182,346.4872 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.8494 >>>>>>> ACTG content number of A's = 83,791,711 bp (28.89%) number of C's = 56,205,081 bp (19.38%) number of T's = 86,493,189 bp (29.82%) number of G's = 63,572,061 bp (21.92%) number of N's = 6,385 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,299,509 number of insertions = 49,545 mapped reads with insertion percentage = 1.52% number of deletions = 100,175 mapped reads with deletion percentage = 3.08% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.0938X std coverageData = 0.9559X There is a 6.87% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 27071479 0.10861148065103517 1.0749899817342392 chr2 243199373 24671210 0.1014443816020858 0.9656797441955048 chr3 198022430 16198344 0.08180055158397966 0.3797145853881723 chr4 191154276 19041876 0.09961522388335169 0.671097555233968 chr5 180915260 17900743 0.09894545656347618 0.3863082779798541 chr6 171115067 23882796 0.13957155508696378 0.7657410742690137 chr7 159138663 16795282 0.10553866473039301 0.9052726835158559 chr8 146364022 14872148 0.10161068134626691 0.47314250500172617 chr9 141213431 12563052 0.08896499370516675 1.2170671195048195 chr10 135534747 16075486 0.1186078578063823 2.87283745437737 chr11 135006516 10516638 0.07789726238102464 0.8491451976207791 chr12 133851895 12851750 0.09601470341529345 0.3821304052052069 chr13 115169878 9896023 0.08592544484591709 0.3597880081645622 chr14 107349540 8553804 0.07968179463088523 0.37258856770616544 chr15 102531392 8407240 0.08199674105663171 0.35114631480608566 chr16 90354753 9529725 0.10547010183293844 1.3313599399187515 chr17 81195210 6176649 0.07607159338586598 0.6193404110935132 chr18 78077248 8125176 0.10406586051803465 1.2555911703046305 chr19 59128983 4209943 0.07119931354138122 0.6238721576832137 chr20 63025520 6207816 0.09849686285809305 0.41023048109721455 chr21 48129895 3805914 0.0790758841256562 0.4514026202357101 chr22 51304566 2997083 0.05841747106875439 0.30047314044877926 chrMT 16571 126070 7.607869169030233 6.707215074050502 chrX 155270560 9045142 0.05825406954157955 0.41922015082496045 chrY 59373566 713491 0.012016980755375212 0.6944161485750219