BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081774.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 = 2,163,594 number of mapped reads = 1,943,598 (89.83%) number of supplementary alignments = 14,110 (0.65%) number of secondary alignments = 0 number of mapped bases = 129,323,042 bp number of sequenced bases = 129,276,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,321 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3385 >>>>>>> ACTG content number of A's = 35,716,436 bp (27.63%) number of C's = 24,441,152 bp (18.91%) number of T's = 40,180,117 bp (31.08%) number of G's = 28,937,577 bp (22.38%) number of N's = 1,533 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,030,946 number of insertions = 9,667 mapped reads with insertion percentage = 0.49% number of deletions = 26,043 mapped reads with deletion percentage = 1.32% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.3675X There is a 3.6% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 10149216 0.04071891961304281 0.6060657649027703 chr2 243199373 11064851 0.04549703752731303 0.46165883259537854 chr3 198022430 8763447 0.044254820022156076 0.2400142798888842 chr4 191154276 8696679 0.04549560272457625 0.2738116424377838 chr5 180915260 7938970 0.0438822573618168 0.23641576140373408 chr6 171115067 7463639 0.043617661091176735 0.27683031047528367 chr7 159138663 7173086 0.04507443926432887 0.5130295676104232 chr8 146364022 6597819 0.04507814768850777 0.43363952282286244 chr9 141213431 5413619 0.03833643132713063 0.35699137332718395 chr10 135534747 6171596 0.04553515712100012 0.43015704396731236 chr11 135006516 5851883 0.043345189353675345 0.323358920943536 chr12 133851895 5809234 0.04340046138308314 0.23693903011984213 chr13 115169878 4136450 0.03591607520848464 0.21173728716928739 chr14 107349540 3963074 0.03691747537995971 0.23314997211517002 chr15 102531392 3658504 0.03568179392317233 0.21542739282189136 chr16 90354753 3595127 0.039789019178659034 0.2660352108074752 chr17 81195210 3296121 0.040595017858812116 0.2489553818975522 chr18 78077248 3490991 0.04471201392754007 0.5952252052137854 chr19 59128983 2495337 0.042201588347968035 0.49376154186028215 chr20 63025520 2545009 0.04038061090174266 0.23960488029674784 chr21 48129895 1703876 0.035401614734459734 0.24085550914502976 chr22 51304566 1371919 0.026740680351920332 0.18241633754912265 chrMT 16571 4577 0.27620541910566654 0.6869916330476366 chrX 155270560 7596808 0.048926261359526234 0.2806674816667135 chrY 59373566 371210 0.0062521088930383596 0.1756643728821394