BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084785.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 = 1,759,277 number of mapped reads = 1,589,299 (90.34%) number of supplementary alignments = 15,751 (0.9%) number of secondary alignments = 0 number of mapped bases = 106,505,454 bp number of sequenced bases = 106,465,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,389 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9654 >>>>>>> ACTG content number of A's = 29,469,712 bp (27.68%) number of C's = 19,642,921 bp (18.45%) number of T's = 33,839,730 bp (31.78%) number of G's = 23,472,634 bp (22.05%) number of N's = 40,742 bp (0.04%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 898,942 number of insertions = 8,141 mapped reads with insertion percentage = 0.51% number of deletions = 24,595 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.2799X There is a 2.88% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 8496455 0.03408799932337982 0.3444671351705764 chr2 243199373 9390986 0.03861435119736102 0.35742645589280403 chr3 198022430 7235480 0.036538689076787915 0.2220591595277546 chr4 191154276 7414462 0.038787842757961634 0.23608698853748028 chr5 180915260 6895536 0.03811472840931163 0.22789599808179672 chr6 171115067 5853952 0.0342106168827319 0.2486640967728368 chr7 159138663 6133157 0.0385397042075187 0.3659764364043611 chr8 146364022 5103956 0.03487165718908709 0.34771356495297184 chr9 141213431 4549408 0.032216538949471456 0.2850554901441559 chr10 135534747 4621970 0.03410173481195933 0.26343982411205596 chr11 135006516 4898919 0.036286537458680886 0.2597619835309688 chr12 133851895 4814217 0.03596674518504202 0.22361025574957802 chr13 115169878 3579646 0.031081443014118675 0.20580333484674276 chr14 107349540 3294134 0.030686056037128803 0.21837003768930524 chr15 102531392 3069246 0.029934695512570435 0.20925669051454918 chr16 90354753 2311956 0.02558754158732524 0.2038963145408241 chr17 81195210 2566507 0.031609093689147424 0.22751530147834798 chr18 78077248 2967987 0.038013468405033946 0.5136617731919725 chr19 59128983 2086925 0.03529445111545382 0.316157909397823 chr20 63025520 2308238 0.03662386284159179 0.22983037898738562 chr21 48129895 1401201 0.029112903736856273 0.2064388017470852 chr22 51304566 1184153 0.02308085015279147 0.17479013581563835 chrMT 16571 11996 0.7239152736708708 1.0026459484596946 chrX 155270560 6075235 0.03912676685135933 0.2448948890754343 chrY 59373566 239732 0.004037689095514324 0.08947860022449783