BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926970.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 30,928,510 number of mapped reads = 30,084,173 (97.27%) number of supplementary alignments = 1,170,492 (3.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,002,832 number of mapped paired reads (second in pair) = 15,081,341 number of mapped paired reads (both in pair) = 29,574,224 number of mapped paired reads (singletons) = 509,949 number of mapped bases = 2,690,836,127 bp number of sequenced bases = 2,688,741,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,436,957 duplication rate = 8.93% >>>>>>> Insert size mean insert size = 370,089.6513 std insert size = 5,942,338.0191 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.4655 >>>>>>> ACTG content number of A's = 769,778,040 bp (28.63%) number of C's = 513,939,466 bp (19.11%) number of T's = 790,635,969 bp (29.41%) number of G's = 614,085,871 bp (22.84%) number of N's = 301,765 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 26,924,036 number of insertions = 479,347 mapped reads with insertion percentage = 1.56% number of deletions = 1,414,170 mapped reads with deletion percentage = 4.58% homopolymer indels = 51.7% >>>>>>> Coverage mean coverageData = 0.8692X std coverageData = 3.2276X There is a 34.29% of reference with a coverageData >= 1X There is a 19.13% of reference with a coverageData >= 2X There is a 10.92% of reference with a coverageData >= 3X There is a 6.75% of reference with a coverageData >= 4X There is a 4.32% of reference with a coverageData >= 5X There is a 2.87% of reference with a coverageData >= 6X There is a 1.96% of reference with a coverageData >= 7X There is a 1.37% of reference with a coverageData >= 8X There is a 0.98% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 220939085 0.8864133782840204 3.2464848284835375 chr2 243199373 237463550 0.9764151406755477 6.2553471204743625 chr3 198022430 180994174 0.9140084484368766 1.8700096380848652 chr4 191154276 166937616 0.8733135323637751 3.003187565249553 chr5 180915260 163685969 0.9047659605939267 1.8509343085146372 chr6 171115067 165390208 0.9665438052862989 2.859313379621061 chr7 159138663 141109498 0.8867078266203606 2.487404173762212 chr8 146364022 135853598 0.9281898388936046 2.1944192909814757 chr9 141213431 111041513 0.7863381847864032 3.651525924136154 chr10 135534747 126312138 0.9319539143714932 4.201310997162711 chr11 135006516 125418265 0.9289793464487299 2.866441600107715 chr12 133851895 126471103 0.9448585169451654 2.0665085973963926 chr13 115169878 81177322 0.7048485542374197 1.6391065914871348 chr14 107349540 78986085 0.7357841030338835 1.765147688106986 chr15 102531392 77538670 0.7562432196375526 1.775031818789096 chr16 90354753 80434760 0.8902106123847187 5.444410574879089 chr17 81195210 65048765 0.801140424416662 2.776535887149844 chr18 78077248 73273957 0.9384802727678107 3.944150191682796 chr19 59128983 40411236 0.6834420947169005 2.2630207593391822 chr20 63025520 59365900 0.9419343148616623 2.1215343293226603 chr21 48129895 33897789 0.704298004389995 2.592795128060241 chr22 51304566 31130112 0.6067707891730338 1.6898725691882595 chrMT 16571 279509 16.86735863858548 14.939918161992827 chrX 155270560 162374059 1.0457491684193063 2.2630865774200553 chrY 59373566 5301246 0.08928629956300756 3.2184404011200045