BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080708.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 = 2,240,492 number of mapped reads = 2,052,452 (91.61%) number of supplementary alignments = 9,179 (0.41%) number of secondary alignments = 0 number of mapped bases = 139,286,682 bp number of sequenced bases = 139,236,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,205 duplication rate = 4.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5439 >>>>>>> ACTG content number of A's = 38,606,818 bp (27.73%) number of C's = 25,989,432 bp (18.67%) number of T's = 44,049,716 bp (31.64%) number of G's = 30,587,844 bp (21.97%) number of N's = 2,190 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,106,627 number of insertions = 9,893 mapped reads with insertion percentage = 0.48% number of deletions = 28,709 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.59% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.3619X There is a 3.68% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% 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 16905310 0.06782454515930775 0.43972549656528553 chr2 243199373 9031984 0.03713818785215371 0.3712260377288474 chr3 198022430 8851612 0.044700047363321414 0.24697036980370135 chr4 191154276 5940353 0.031076223479301085 0.2131232737736797 chr5 180915260 6224183 0.034403858469429276 0.2154695358485936 chr6 171115067 8395207 0.049061763801313885 0.3473583329181212 chr7 159138663 8785214 0.05520477446766032 0.8841827368112898 chr8 146364022 16444437 0.11235300024756084 0.47811829432338687 chr9 141213431 4277855 0.030293541979020396 0.2555250352180991 chr10 135534747 6644393 0.049023539328995835 0.3203827594439204 chr11 135006516 5862953 0.0434271853959997 0.27517076568574667 chr12 133851895 4307170 0.032178625487521116 0.20893761917661338 chr13 115169878 3014371 0.026173258601524262 0.18951057946226052 chr14 107349540 2740111 0.02552513033591015 0.19224965610058178 chr15 102531392 2534357 0.024717863968919878 0.1839232391647372 chr16 90354753 3494678 0.03867730123726861 0.24578525723155326 chr17 81195210 2284763 0.02813913530120804 0.20397408126458555 chr18 78077248 4225757 0.054122770823069995 0.3826597779837965 chr19 59128983 2324623 0.03931444246216784 0.30508974081099877 chr20 63025520 3646342 0.057855008574304506 0.28573091944011214 chr21 48129895 2015068 0.04186728435621977 0.24843445086512955 chr22 51304566 1448349 0.028230411304911926 0.19401532459902948 chrMT 16571 394342 23.79711544264076 14.776567896037507 chrX 155270560 9224639 0.05941009680135114 0.30800340466019704 chrY 59373566 268611 0.004524084000614011 0.10065394761870201