BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084800.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,188,967 number of mapped reads = 1,989,025 (90.87%) number of supplementary alignments = 20,664 (0.94%) number of secondary alignments = 0 number of mapped bases = 132,582,455 bp number of sequenced bases = 132,533,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,524 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1952 >>>>>>> ACTG content number of A's = 35,847,987 bp (27.05%) number of C's = 24,970,005 bp (18.84%) number of T's = 41,432,089 bp (31.26%) number of G's = 30,264,853 bp (22.84%) number of N's = 18,463 bp (0.01%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,026,562 number of insertions = 10,412 mapped reads with insertion percentage = 0.52% number of deletions = 30,295 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.3037X There is a 3.61% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 10360313 0.041565846289305736 0.3499450410008572 chr2 243199373 10862417 0.044664658736599624 0.51086975401616 chr3 198022430 10997869 0.05553850137077906 0.27225744147768827 chr4 191154276 8154191 0.04265764371391828 0.2417126823825439 chr5 180915260 7232553 0.039977572925578526 0.2302694653934499 chr6 171115067 7604329 0.04443985636869721 0.26393211232151736 chr7 159138663 7175676 0.04509071437906953 0.3340595723512789 chr8 146364022 8508264 0.05813084311115747 0.3337495558920577 chr9 141213431 9644316 0.06829602490148405 0.3751865493140805 chr10 135534747 3834224 0.028289601632561428 0.21762008816050343 chr11 135006516 6009721 0.044514303294812825 0.3051277748383096 chr12 133851895 5243455 0.03917355820774895 0.2311090556666107 chr13 115169878 3534341 0.030688067586561132 0.20155108122101498 chr14 107349540 2695514 0.0251096930643578 0.1892503589693825 chr15 102531392 3201678 0.031226319447608786 0.2153812958575237 chr16 90354753 2412310 0.026698208117507664 0.2006820870828883 chr17 81195210 3666807 0.04516038569270281 0.25910048834374194 chr18 78077248 5158545 0.06606975952840961 0.45241090194638317 chr19 59128983 2569598 0.043457503742284895 0.29653034851934584 chr20 63025520 2804863 0.04450360742759441 0.24604911908262808 chr21 48129895 1194416 0.024816509572688657 0.188068134191842 chr22 51304566 1348619 0.02628652974084217 0.1839837701385034 chrMT 16571 21042 1.2698087019491884 1.3793091782206464 chrX 155270560 8052476 0.05186093229779039 0.28086381281031875 chrY 59373566 294918 0.004967159964756033 0.10074845802826779