BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054613.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,117,844 number of mapped reads = 10,044,085 (76.57%) number of supplementary alignments = 304 (0%) number of secondary alignments = 0 number of mapped bases = 474,512,144 bp number of sequenced bases = 474,417,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,392,173 duplication rate = 16.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3246 >>>>>>> ACTG content number of A's = 139,545,284 bp (29.41%) number of C's = 92,842,299 bp (19.57%) number of T's = 141,075,489 bp (29.74%) number of G's = 100,686,103 bp (21.22%) number of N's = 268,182 bp (0.06%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 3,100,344 number of insertions = 19,181 mapped reads with insertion percentage = 0.19% number of deletions = 63,500 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.1533X std coverageData = 1.0859X There is a 6.41% of reference with a coverageData >= 1X There is a 2.73% of reference with a coverageData >= 2X There is a 1.56% of reference with a coverageData >= 3X There is a 1.02% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 43640930 0.1750885507322367 1.2252469710379223 chr2 243199373 40599775 0.1669402947021578 1.2496947416963942 chr3 198022430 32602508 0.16464048037386472 1.080687401273303 chr4 191154276 30805489 0.16115511326568493 1.1074190623932267 chr5 180915260 23880754 0.13199966658423395 0.8939477046225518 chr6 171115067 23890812 0.1396184007571934 1.0111397858172781 chr7 159138663 30492916 0.19161224196033366 1.2691539592704746 chr8 146364022 24634321 0.16830858200931373 1.1399034780450192 chr9 141213431 23728631 0.16803381117480248 1.1246058338533342 chr10 135534747 20142499 0.1486150189958299 1.0430101835398995 chr11 135006516 20564421 0.15232169238409204 1.045708573231541 chr12 133851895 18503266 0.13823686246653438 0.9303871275378516 chr13 115169878 13898556 0.12067874205788427 0.8555500555901013 chr14 107349540 9408382 0.08764249944620163 0.8939985701955376 chr15 102531392 12665117 0.12352428610351843 0.8902795267900915 chr16 90354753 13057498 0.144513681532614 1.0325090215406536 chr17 81195210 9195930 0.11325705050827506 0.8484566148980359 chr18 78077248 16851643 0.21583295302621322 1.3338681603985036 chr19 59128983 8946985 0.15131302021548385 1.1081772040134417 chr20 63025520 8996180 0.14273868743962764 1.0140324610626847 chr21 48129895 4897350 0.10175276717308442 0.9235222935033959 chr22 51304566 4640481 0.09044966874878155 0.7237174032762805 chrMT 16571 48507 2.9272222557479934 5.946440308583665 chrX 155270560 37298352 0.24021522173939477 1.415626820867466 chrY 59373566 1120841 0.018877778033409683 0.3787640815542847