BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080658.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 = 1,218,225 number of mapped reads = 1,122,645 (92.15%) number of supplementary alignments = 10,764 (0.88%) number of secondary alignments = 0 number of mapped bases = 75,628,452 bp number of sequenced bases = 75,599,649 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,988 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3036 >>>>>>> ACTG content number of A's = 21,173,564 bp (28.01%) number of C's = 13,709,126 bp (18.13%) number of T's = 24,249,188 bp (32.08%) number of G's = 16,464,446 bp (21.78%) number of N's = 3,325 bp (0%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 513,768 number of insertions = 5,941 mapped reads with insertion percentage = 0.53% number of deletions = 17,763 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.76% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2058X There is a 2.18% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9023409 0.03620215253144746 0.259000657315707 chr2 243199373 4907973 0.02018086206167974 0.2606272577054275 chr3 198022430 4688826 0.023678257054011508 0.16895528570058593 chr4 191154276 3960765 0.02072025320532197 0.15872599088525283 chr5 180915260 3442470 0.019028079776133865 0.15054182966949636 chr6 171115067 4697330 0.027451293929598847 0.21668950505014042 chr7 159138663 4824059 0.030313557428844302 0.3561251645471967 chr8 146364022 9086834 0.0620837954289067 0.30796516667584484 chr9 141213431 2361312 0.016721582240998026 0.1572266512534474 chr10 135534747 3653602 0.02695693968425676 0.18771472656572566 chr11 135006516 3102403 0.02297965381167232 0.17258346699367738 chr12 133851895 2403840 0.0179589538123461 0.14732765703468784 chr13 115169878 1543992 0.013406213732378878 0.12626469083999275 chr14 107349540 1483838 0.013822490529535571 0.1309211183404204 chr15 102531392 1332278 0.012993854604061165 0.13070293487105528 chr16 90354753 1768765 0.01957578258224003 0.1546426308236144 chr17 81195210 1097887 0.013521573501688092 0.12966275919784975 chr18 78077248 2448701 0.03136254238878911 0.22859520834139962 chr19 59128983 1126873 0.019057878942379237 0.1734022583316915 chr20 63025520 1882043 0.02986160209388197 0.189794486346339 chr21 48129895 1051307 0.021843118502544 0.16337466090929786 chr22 51304566 643989 0.012552274587022138 0.1219525134664745 chrMT 16571 12744 0.76905437209583 1.0352504553315192 chrX 155270560 4935200 0.03178451858484957 0.2007660193208576 chrY 59373566 148012 0.002492893891534155 0.05615632730189064