BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818994.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,528,243 number of mapped reads = 2,496,068 (98.73%) number of supplementary alignments = 39,362 (1.56%) number of secondary alignments = 0 number of mapped bases = 231,061,700 bp number of sequenced bases = 230,923,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,219,697 duplication rate = 41.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1262 >>>>>>> ACTG content number of A's = 65,944,721 bp (28.56%) number of C's = 48,932,325 bp (21.19%) number of T's = 66,353,797 bp (28.73%) number of G's = 49,682,143 bp (21.51%) number of N's = 10,943 bp (0%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,466,691 number of insertions = 36,800 mapped reads with insertion percentage = 1.43% number of deletions = 74,276 mapped reads with deletion percentage = 2.91% homopolymer indels = 40.76% >>>>>>> Coverage mean coverageData = 0.0746X std coverageData = 0.8773X There is a 3.14% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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% 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 22753718 0.0912885107716542 1.5058817264140638 chr2 243199373 18304076 0.07526366443387171 1.2642933194698824 chr3 198022430 13619259 0.06877634518473488 0.5130752926013874 chr4 191154276 12770159 0.0668055105395602 0.5769615107085018 chr5 180915260 12459161 0.06886738575839318 0.5369603371850494 chr6 171115067 9801390 0.05727952641365006 0.5806612506120924 chr7 159138663 11515731 0.07236287387936645 1.1213761000087665 chr8 146364022 21123195 0.1443195855877751 0.8450913536919967 chr9 141213431 9781227 0.06926555732506776 0.8279805617714447 chr10 135534747 11791141 0.0869971816157225 1.0198623734110404 chr11 135006516 7776643 0.05760198270726429 0.560658892672828 chr12 133851895 10810839 0.08076717180582314 0.5690514382653029 chr13 115169878 5020449 0.043591684624342486 0.40184967637843333 chr14 107349540 5380201 0.05011852868675543 0.46664511191914015 chr15 102531392 5995621 0.058475954369175055 0.47721814855264333 chr16 90354753 7406929 0.08197608597303122 1.107963527409653 chr17 81195210 7996382 0.09848342038896137 0.6985261799217936 chr18 78077248 5391903 0.0690585687651286 0.9070438218730884 chr19 59128983 4737234 0.08011695381265056 1.3672858563371781 chr20 63025520 6628343 0.10516919178136094 0.6807501641156274 chr21 48129895 3307672 0.06872385655526571 0.5859645441237757 chr22 51304566 1898727 0.03700892821118495 0.4244165632554299 chrMT 16571 25378 1.5314706414821073 2.5790139215280528 chrX 155270560 13903954 0.08954662107227539 0.6913934025785378 chrY 59373566 862368 0.014524443419820867 0.9478752197899792