BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084787.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 = 1,726,713 number of mapped reads = 1,532,646 (88.76%) number of supplementary alignments = 21,745 (1.26%) number of secondary alignments = 0 number of mapped bases = 101,935,051 bp number of sequenced bases = 101,900,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,862 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2073 >>>>>>> ACTG content number of A's = 28,858,406 bp (28.32%) number of C's = 19,239,220 bp (18.88%) number of T's = 30,707,629 bp (30.13%) number of G's = 23,069,465 bp (22.64%) number of N's = 25,820 bp (0.03%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 878,092 number of insertions = 9,037 mapped reads with insertion percentage = 0.58% number of deletions = 20,757 mapped reads with deletion percentage = 1.34% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.4574X There is a 3% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8179620 0.03281684903003712 0.9546891265332519 chr2 243199373 8723290 0.035868883592886563 0.512217355458629 chr3 198022430 6776097 0.03421883571472181 0.1973598917802655 chr4 191154276 6531710 0.03416983463137387 0.21175589971802297 chr5 180915260 6213752 0.034346201641586235 0.20182277233796833 chr6 171115067 5915597 0.03457087154107826 0.27688695598763075 chr7 159138663 5734942 0.036037389606572226 0.6489656957783682 chr8 146364022 5285941 0.03611502968946836 0.6801751197006224 chr9 141213431 4280985 0.030315707009484105 0.40204922340157107 chr10 135534747 4777340 0.035248082914117955 0.39728240407633447 chr11 135006516 4660911 0.034523600327557524 0.37558695390464536 chr12 133851895 4570614 0.03414680083535612 0.2052125509099701 chr13 115169878 3156476 0.027407131576539484 0.17561659654117165 chr14 107349540 3078587 0.0286781573540045 0.2116455961117548 chr15 102531392 2819588 0.027499753441365547 0.18850382388845852 chr16 90354753 2816944 0.03117648940947246 0.23952433191153816 chr17 81195210 2615513 0.03221265146059724 0.237635579873499 chr18 78077248 2763492 0.03539433152152084 0.7807130775370087 chr19 59128983 2104111 0.035585103839854644 0.6884254385769927 chr20 63025520 1977588 0.031377575306003026 0.19823758116205745 chr21 48129895 1320000 0.02742578183476195 0.19184961615818893 chr22 51304566 1079735 0.021045592706115085 0.15159233234776523 chrMT 16571 13718 0.827831754269507 0.9984540580318635 chrX 155270560 6235520 0.04015906170493621 0.2789635618646006 chrY 59373566 302980 0.005102944296793627 0.13945127702223786