BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082927.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 = 2,008,345 number of mapped reads = 1,780,362 (88.65%) number of supplementary alignments = 16,405 (0.82%) number of secondary alignments = 0 number of mapped bases = 117,986,223 bp number of sequenced bases = 117,942,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,876 duplication rate = 4.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6288 >>>>>>> ACTG content number of A's = 31,599,356 bp (26.79%) number of C's = 22,001,105 bp (18.65%) number of T's = 37,175,053 bp (31.52%) number of G's = 27,161,111 bp (23.03%) number of N's = 5,528 bp (0%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 840,159 number of insertions = 9,095 mapped reads with insertion percentage = 0.51% number of deletions = 26,836 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.2687X There is a 3.12% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 11211887 0.044982383414001605 0.29409843021197346 chr2 243199373 11984902 0.04928015172144379 0.4313697015148834 chr3 198022430 8117962 0.04099516403268054 0.23865191548778508 chr4 191154276 7944346 0.04155986549837891 0.24556552726587705 chr5 180915260 5975243 0.03302785514057797 0.21542799289164627 chr6 171115067 8569009 0.050077466293485424 0.3115476103210945 chr7 159138663 6990120 0.04392471237489283 0.2723251527671467 chr8 146364022 9236053 0.06310330143838218 0.31993894538249223 chr9 141213431 3306115 0.023412185204961133 0.20446912707289444 chr10 135534747 4229544 0.031206344451286724 0.2129305899609579 chr11 135006516 5031005 0.03726490505095324 0.2694968991542626 chr12 133851895 3696610 0.027617165972883686 0.196806551883152 chr13 115169878 2750682 0.02388369292185931 0.1851824003269434 chr14 107349540 2590416 0.024130666978172427 0.18756044202865585 chr15 102531392 2266758 0.02210794134151617 0.18706196781048892 chr16 90354753 5029277 0.05566145479917365 0.286263904031334 chr17 81195210 3142143 0.038698625202151705 0.24051913207470382 chr18 78077248 3019367 0.03867153463195834 0.34252609120739763 chr19 59128983 1715036 0.029004997430786186 0.24408969356140098 chr20 63025520 2241406 0.03556346698924499 0.22519435209665356 chr21 48129895 2335012 0.04851479522238725 0.26509824091364026 chr22 51304566 1693982 0.03301815280924509 0.21565963961400872 chrMT 16571 172110 10.386216884919438 7.340272005207008 chrX 155270560 4559541 0.029365135283855485 0.20772705489088333 chrY 59373566 177697 0.0029928638613351943 0.06474419231656775