BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081116.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 = 3,951,715 number of mapped reads = 3,621,888 (91.65%) number of supplementary alignments = 27,143 (0.69%) number of secondary alignments = 0 number of mapped bases = 243,175,999 bp number of sequenced bases = 243,086,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 198,874 duplication rate = 4.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.236 >>>>>>> ACTG content number of A's = 68,730,192 bp (28.27%) number of C's = 46,878,645 bp (19.28%) number of T's = 74,831,827 bp (30.78%) number of G's = 52,642,802 bp (21.66%) number of N's = 2,746 bp (0%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,135,068 number of insertions = 17,860 mapped reads with insertion percentage = 0.49% number of deletions = 50,697 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.0786X std coverageData = 0.5463X There is a 5.94% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 19776515 0.07934389459354647 0.7889776797220721 chr2 243199373 17371240 0.07142798020289304 0.5927317752322471 chr3 198022430 20745778 0.10476478851410924 0.414081110356713 chr4 191154276 15226009 0.07965298667972251 0.40420783005816274 chr5 180915260 13224764 0.07309921783270244 0.34407685761039464 chr6 171115067 19749777 0.11541810634361029 0.6235267856649215 chr7 159138663 11829224 0.07433280999727891 0.5812579118441508 chr8 146364022 16980565 0.1160159769318173 0.6595437364373191 chr9 141213431 12103452 0.0857103457814859 0.6827135574669213 chr10 135534747 11305894 0.08341694104464592 0.5395042855211037 chr11 135006516 10760132 0.07970083458786538 0.49041426932579485 chr12 133851895 12125161 0.09058639774954251 0.4037846475077265 chr13 115169878 6518761 0.056601266869450016 0.29621524198558824 chr14 107349540 7094163 0.06608470795496656 0.4428064943445715 chr15 102531392 6303266 0.06147645006126514 0.3207072755564095 chr16 90354753 6745373 0.07465432394021375 0.442265538794644 chr17 81195210 5595393 0.0689128459671451 0.34973807506215804 chr18 78077248 5532135 0.07085463616750426 1.1763383373684018 chr19 59128983 5049199 0.08539296202676105 0.6789583401345581 chr20 63025520 3795880 0.06022766650715456 0.33133762209304884 chr21 48129895 4434766 0.0921416097001666 0.48723815766801704 chr22 51304566 2436377 0.04748850229041992 0.27158762116494156 chrMT 16571 215591 13.010138193229135 8.385058904738578 chrX 155270560 7611324 0.04901974978386115 0.33273335931705966 chrY 59373566 645260 0.010867799316618442 0.25939051576345473