BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083656.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 = 1,905,391 number of mapped reads = 1,706,124 (89.54%) number of supplementary alignments = 15,384 (0.81%) number of secondary alignments = 0 number of mapped bases = 113,230,995 bp number of sequenced bases = 113,188,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,944 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3607 >>>>>>> ACTG content number of A's = 30,130,930 bp (26.62%) number of C's = 21,472,089 bp (18.97%) number of T's = 35,199,062 bp (31.1%) number of G's = 26,381,104 bp (23.31%) number of N's = 5,661 bp (0.01%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 789,744 number of insertions = 8,645 mapped reads with insertion percentage = 0.5% number of deletions = 25,884 mapped reads with deletion percentage = 1.5% homopolymer indels = 48% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.2968X There is a 3.01% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% 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 11013758 0.04418748469236512 0.4641682836474698 chr2 243199373 8885050 0.03653401688663071 0.4467583592530924 chr3 198022430 7498365 0.03786624070818644 0.2308602999416402 chr4 191154276 5788452 0.030281572147515028 0.2083153211259957 chr5 180915260 6155660 0.03402510103348938 0.21687390314852464 chr6 171115067 7605405 0.044446144535010466 0.30206106961780815 chr7 159138663 6967791 0.04378440077757848 0.3488975858519778 chr8 146364022 6152696 0.04203694265794363 0.2806500827231944 chr9 141213431 5166565 0.036586923520043925 0.2630307683262394 chr10 135534747 5644424 0.04164558627906687 0.27575109476263565 chr11 135006516 4207089 0.031162118130653782 0.24387849411709517 chr12 133851895 4743242 0.03543649494091959 0.22189455540721578 chr13 115169878 3748106 0.03254415186582033 0.2125839485265958 chr14 107349540 2150486 0.02003255905893961 0.16988899380999334 chr15 102531392 3019020 0.02944483578258647 0.21011751993934122 chr16 90354753 3447758 0.038158014775382096 0.2402903908104593 chr17 81195210 3114601 0.038359418000150504 0.23991890719678505 chr18 78077248 2960247 0.03791433581265569 0.418493888832517 chr19 59128983 3211743 0.0543175755280621 0.3660481577414968 chr20 63025520 3014542 0.04783049786816515 0.26394032347074464 chr21 48129895 2434274 0.05057717246214645 0.274965952430392 chr22 51304566 1121536 0.02186035449554334 0.17386094168896815 chrMT 16571 3744 0.225936877677871 0.5585663784452535 chrX 155270560 4959275 0.03193957051484841 0.21804828109712734 chrY 59373566 217166 0.0036576209689005374 0.08525547183273437