BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084786.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 = 1,095,256 number of mapped reads = 983,186 (89.77%) number of supplementary alignments = 14,991 (1.37%) number of secondary alignments = 0 number of mapped bases = 65,452,304 bp number of sequenced bases = 65,428,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,814 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8252 >>>>>>> ACTG content number of A's = 18,724,781 bp (28.62%) number of C's = 12,154,787 bp (18.58%) number of T's = 19,872,669 bp (30.37%) number of G's = 14,655,875 bp (22.4%) number of N's = 20,705 bp (0.03%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 558,366 number of insertions = 5,782 mapped reads with insertion percentage = 0.58% number of deletions = 14,064 mapped reads with deletion percentage = 1.41% homopolymer indels = 44.08% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.3081X There is a 1.96% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5212665 0.02091334809552992 0.6427998267979201 chr2 243199373 5597411 0.02301572956769095 0.3316335751311247 chr3 198022430 4393696 0.022187870333678868 0.15698025515763223 chr4 191154276 4270685 0.02234156143072625 0.15950897505495196 chr5 180915260 4040402 0.022333118831435225 0.1578738164902739 chr6 171115067 3844365 0.022466548781469958 0.20016254820387755 chr7 159138663 3693458 0.023209055111893206 0.4199291996891004 chr8 146364022 3367252 0.023006008949385117 0.40528539173517136 chr9 141213431 2782475 0.019704039341696896 0.2819034685679076 chr10 135534747 3106009 0.02291669899232556 0.27514850748271036 chr11 135006516 2986975 0.022124672856530865 0.24894226768914765 chr12 133851895 2943533 0.021990969944803547 0.1612701593794126 chr13 115169878 2069847 0.017972121147857775 0.138186800427493 chr14 107349540 1990606 0.018543218722688517 0.15739124182702185 chr15 102531392 1800382 0.017559324660295257 0.14292824930352652 chr16 90354753 1767346 0.019560077819038475 0.17676711043146198 chr17 81195210 1630815 0.020085113395236 0.1718718726412758 chr18 78077248 1777791 0.02276964218820827 0.516562349027991 chr19 59128983 1310161 0.02215767857870987 0.4944402629194111 chr20 63025520 1246946 0.01978477924497886 0.15262785339933083 chr21 48129895 834720 0.01734306713114583 0.14931535444047014 chr22 51304566 643841 0.012549389853526877 0.11509596622980738 chrMT 16571 7956 0.4801158650654758 0.7251675577412344 chrX 155270560 3949350 0.02543527890927939 0.2034508365654923 chrY 59373566 183617 0.003092571532590783 0.08167014938410823