BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085099.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 = 1,425,781 number of mapped reads = 1,112,649 (78.04%) number of supplementary alignments = 6,553 (0.46%) number of secondary alignments = 0 number of mapped bases = 71,708,141 bp number of sequenced bases = 71,682,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,132 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4243 >>>>>>> ACTG content number of A's = 21,585,991 bp (30.11%) number of C's = 13,416,608 bp (18.72%) number of T's = 20,861,474 bp (29.1%) number of G's = 15,816,773 bp (22.07%) number of N's = 1,555 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 656,544 number of insertions = 5,598 mapped reads with insertion percentage = 0.5% number of deletions = 15,905 mapped reads with deletion percentage = 1.41% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2066X There is a 2.15% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 7442329 0.029858818285552036 0.3241529824463763 chr2 243199373 7313201 0.030070805322347603 0.2389561166271375 chr3 198022430 4210006 0.021260248144616748 0.15473518402721517 chr4 191154276 4264913 0.022311365925186 0.15885571347261918 chr5 180915260 3508507 0.01939309597211424 0.14568171098006216 chr6 171115067 4712696 0.02754109315224708 0.19331440016172316 chr7 159138663 6301059 0.03959477151067934 0.25622920477818967 chr8 146364022 4486822 0.03065522482020889 0.29343099581089255 chr9 141213431 1546917 0.010954460840201524 0.15304295713266644 chr10 135534747 4283870 0.03160717155431736 0.27891098722245444 chr11 135006516 3341647 0.024751746056464415 0.2120740107160066 chr12 133851895 2936022 0.021934855685083875 0.15687818994332525 chr13 115169878 1547233 0.013434354771132084 0.12039236788313594 chr14 107349540 2385586 0.02222260104700961 0.15968591811542798 chr15 102531392 1233879 0.012034158280031935 0.11416479046598609 chr16 90354753 1822975 0.020175751019982313 0.15813880442500902 chr17 81195210 1038103 0.012785273909630876 0.1289325186026947 chr18 78077248 2177933 0.027894592288908542 0.2848200864375391 chr19 59128983 1079192 0.018251489290793316 0.21816383625452507 chr20 63025520 1629708 0.025857906448054694 0.17157059618652 chr21 48129895 1055996 0.02194054235937976 0.15916640998584683 chr22 51304566 475069 0.009259780113918125 0.10005317315241954 chrMT 16571 2598 0.15677991672198419 0.3917166107088145 chrX 155270560 2772378 0.017855142661944413 0.15108957583738766 chrY 59373566 139502 0.002349564114104246 0.06013320118741798