BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084807.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 = 1,791,230 number of mapped reads = 1,635,151 (91.29%) number of supplementary alignments = 17,299 (0.97%) number of secondary alignments = 0 number of mapped bases = 110,137,920 bp number of sequenced bases = 110,095,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,922 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3241 >>>>>>> ACTG content number of A's = 30,581,434 bp (27.78%) number of C's = 20,383,360 bp (18.51%) number of T's = 34,937,325 bp (31.73%) number of G's = 24,177,123 bp (21.96%) number of N's = 15,869 bp (0.01%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 816,219 number of insertions = 8,841 mapped reads with insertion percentage = 0.54% number of deletions = 25,505 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.69% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.2502X There is a 2.98% of reference with a coverageData >= 1X There is a 0.45% 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 8958508 0.0359417680247224 0.26438734517773815 chr2 243199373 9748457 0.04008421929607524 0.37148367494916334 chr3 198022430 8348911 0.04216144100443571 0.24005075459006495 chr4 191154276 6677607 0.03493307677825632 0.2188224122235853 chr5 180915260 5916181 0.03270139290627004 0.21029292400315397 chr6 171115067 6079696 0.03552986950003649 0.2311464613574181 chr7 159138663 6215109 0.03905467648675671 0.24656825976696867 chr8 146364022 6091313 0.04161755680641244 0.29310206356774493 chr9 141213431 7658723 0.0542350890121776 0.30432266998756924 chr10 135534747 3165373 0.023354697375131413 0.18641103972589773 chr11 135006516 4252766 0.03150044994865285 0.22804280688008843 chr12 133851895 4537003 0.03389569493954493 0.21545583955313935 chr13 115169878 3117746 0.02707084572929738 0.19229290791820075 chr14 107349540 2319626 0.021608159662351602 0.1756518319880883 chr15 102531392 2700836 0.02634155205851492 0.1917812667241893 chr16 90354753 2294470 0.025394015520135392 0.19073065233515557 chr17 81195210 3296663 0.0406016931294346 0.23548382261450498 chr18 78077248 4681812 0.059963845037161144 0.3898168254508431 chr19 59128983 2167524 0.0366575559062127 0.24608010115920523 chr20 63025520 2206388 0.03500785078806173 0.21987286767343187 chr21 48129895 996238 0.020698943972348165 0.17029027240909403 chr22 51304566 914588 0.01782663944569768 0.15353795576562695 chrMT 16571 25031 1.5105304447528816 1.591590842839165 chrX 155270560 7519085 0.04842569641018877 0.26294835985052795 chrY 59373566 248266 0.004181423093233106 0.09198992190189992