BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084804.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 = 2,072,403 number of mapped reads = 1,840,404 (88.81%) number of supplementary alignments = 24,627 (1.19%) number of secondary alignments = 0 number of mapped bases = 122,700,391 bp number of sequenced bases = 122,653,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,318 duplication rate = 4.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4871 >>>>>>> ACTG content number of A's = 33,552,736 bp (27.36%) number of C's = 22,839,688 bp (18.62%) number of T's = 38,713,310 bp (31.56%) number of G's = 27,530,462 bp (22.45%) number of N's = 17,361 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 971,694 number of insertions = 9,845 mapped reads with insertion percentage = 0.53% number of deletions = 28,366 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.2962X There is a 3.18% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.12% 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 9586992 0.03846326224398855 0.3469990194578388 chr2 243199373 10386803 0.04270900402362468 0.4885250084948549 chr3 198022430 9314849 0.04703936316709173 0.26164766560151304 chr4 191154276 7559259 0.03954533039062124 0.24255412576171664 chr5 180915260 7152886 0.03953721759015796 0.24071284355563705 chr6 171115067 6771396 0.039572178643976455 0.25855746205168334 chr7 159138663 6884589 0.043261573713233976 0.2759667063276829 chr8 146364022 6415161 0.043830177063595585 0.32379088174008175 chr9 141213431 9553776 0.06765486775829418 0.37566852613306767 chr10 135534747 4498567 0.03319124504655622 0.2330411748840388 chr11 135006516 4798597 0.03554344739923516 0.2639901558698947 chr12 133851895 4929499 0.036828010541053606 0.2330645532610677 chr13 115169878 3478320 0.030201646996621808 0.20994305786696715 chr14 107349540 2701754 0.02516782093337335 0.19905232496536004 chr15 102531392 2415188 0.023555595538974055 0.19002645516092537 chr16 90354753 2521112 0.027902372772797022 0.21024368513824077 chr17 81195210 3509200 0.043219298281265604 0.26077745498767096 chr18 78077248 5722186 0.07328877677655851 0.4868574561892235 chr19 59128983 2620488 0.04431816457928931 0.304335485745534 chr20 63025520 2506580 0.039770873766690064 0.24244437682841044 chr21 48129895 1149910 0.023891803628493267 0.19177246293858652 chr22 51304566 1268464 0.02472419316440568 0.18793487124122893 chrMT 16571 16036 0.9677146822762658 1.2302320775520734 chrX 155270560 6670666 0.042961563351095015 0.26110557056922357 chrY 59373566 268113 0.004515696429619875 0.09868428939853248