BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708525.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,364,858 number of mapped reads = 2,345,116 (69.69%) number of supplementary alignments = 526 (0.02%) number of secondary alignments = 0 number of mapped bases = 112,637,393 bp number of sequenced bases = 112,615,990 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,465 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0447 >>>>>>> ACTG content number of A's = 32,550,626 bp (28.9%) number of C's = 21,042,520 bp (18.69%) number of T's = 35,866,717 bp (31.85%) number of G's = 23,154,435 bp (20.56%) number of N's = 1,692 bp (0%) GC percentage = 39.25% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 536,583 number of insertions = 5,332 mapped reads with insertion percentage = 0.23% number of deletions = 13,827 mapped reads with deletion percentage = 0.59% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0364X std coverageData = 0.3194X There is a 3.15% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9452775 0.0379247801352519 0.5536325966981794 chr2 243199373 9799784 0.04029526835992295 0.2999241502007608 chr3 198022430 7845550 0.03961950168978332 0.2261268045727185 chr4 191154276 7118988 0.037242106998433035 0.22233525532033796 chr5 180915260 7150586 0.039524504455843025 0.22691003436734714 chr6 171115067 7015118 0.04099649506609491 0.2781886419821348 chr7 159138663 6364163 0.03999130619816757 0.40762115779153935 chr8 146364022 5945472 0.04062113023923324 0.6132255778499743 chr9 141213431 4770138 0.033779633893322794 0.23844492702569287 chr10 135534747 5160955 0.03807846411518369 0.2626866111372638 chr11 135006516 5260132 0.03896206017196977 0.274417993331291 chr12 133851895 5313386 0.03969600878642771 0.22898947684702012 chr13 115169878 3671039 0.03187499252191619 0.20296409968819967 chr14 107349540 3730012 0.034746418102956006 0.21581397662989904 chr15 102531392 3448447 0.033633084782463504 0.20837962864845638 chr16 90354753 3165135 0.035030088566563845 0.21622266295927056 chr17 81195210 3098525 0.038161426025008126 0.25081941315495104 chr18 78077248 3040366 0.03894048622205537 0.3641526954121983 chr19 59128983 2085279 0.03526661366727718 0.4074605934383524 chr20 63025520 2255118 0.035781029652750186 0.21378089241522144 chr21 48129895 1435291 0.02982119532984645 0.21767333793843585 chr22 51304566 1300459 0.025347821868330393 0.19069006981577566 chrMT 16571 153570 9.267394846418442 6.570494952810634 chrX 155270560 3380230 0.02176993500892893 0.1851410893878188 chrY 59373566 676875 0.011400275334649766 0.12994613714529057