BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053678.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 = 8,237,269 number of mapped reads = 7,125,379 (86.5%) number of supplementary alignments = 210 (0%) number of secondary alignments = 0 number of mapped bases = 336,892,030 bp number of sequenced bases = 336,823,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,737,465 duplication rate = 17.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2002 >>>>>>> ACTG content number of A's = 98,688,046 bp (29.3%) number of C's = 67,267,797 bp (19.97%) number of T's = 98,602,777 bp (29.27%) number of G's = 72,253,657 bp (21.45%) number of N's = 11,326 bp (0%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,549,816 number of insertions = 13,026 mapped reads with insertion percentage = 0.18% number of deletions = 45,585 mapped reads with deletion percentage = 0.64% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.1088X std coverageData = 0.8727X There is a 4.57% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 1.14% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.01% 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 27788460 0.1114880271451761 0.9589977399649888 chr2 243199373 34866083 0.1433641977358223 1.0602852155117362 chr3 198022430 20805127 0.10506449698652824 0.7965019448744033 chr4 191154276 15729951 0.08228929704925879 0.7090845733471981 chr5 180915260 17209317 0.09512363412572272 0.7544806537824811 chr6 171115067 19803700 0.11573323347382379 0.913346013534187 chr7 159138663 16970581 0.10664021350989986 0.8490413606032969 chr8 146364022 22378200 0.1528941313186925 1.078205118521839 chr9 141213431 17837228 0.12631396230292005 0.9385697053463696 chr10 135534747 11308013 0.0834325754118241 0.7623009721504642 chr11 135006516 16033673 0.1187622158918611 0.9149065209345318 chr12 133851895 17830367 0.1332096717793947 0.9335301629909598 chr13 115169878 9247996 0.0802987392241572 0.7100818776500639 chr14 107349540 10525446 0.09804835679780277 0.8545989167042783 chr15 102531392 7767389 0.07575620352447765 0.6661997624681459 chr16 90354753 7724310 0.08548869587413957 0.7542382749605333 chr17 81195210 7716867 0.09504091435935691 0.740642018968116 chr18 78077248 9847705 0.12612771648918775 0.960180363417502 chr19 59128983 7044431 0.11913668462723263 0.9672227743584653 chr20 63025520 6969843 0.11058763180375188 0.8387459863497634 chr21 48129895 3906246 0.08116049287038753 0.755334330520242 chr22 51304566 4673627 0.09109573210306467 0.7546430096319351 chrMT 16571 20668 1.2472391527367086 4.51707116496211 chrX 155270560 22090682 0.14227218604737435 1.0009426512302553 chrY 59373566 796120 0.013408660682432313 0.31368700705679037