BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081140.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 = 2,462,865 number of mapped reads = 2,144,708 (87.08%) number of supplementary alignments = 18,735 (0.76%) number of secondary alignments = 0 number of mapped bases = 143,477,716 bp number of sequenced bases = 143,427,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,631 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.681 >>>>>>> ACTG content number of A's = 41,041,879 bp (28.62%) number of C's = 26,436,524 bp (18.43%) number of T's = 45,029,381 bp (31.4%) number of G's = 30,876,892 bp (21.53%) number of N's = 42,336 bp (0.03%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,190,859 number of insertions = 11,383 mapped reads with insertion percentage = 0.53% number of deletions = 30,751 mapped reads with deletion percentage = 1.42% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.3724X There is a 4.02% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.01% 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 11845201 0.047523255719390964 0.7072768085413551 chr2 243199373 12015414 0.04940561257121333 0.42548576426641843 chr3 198022430 9797303 0.04947572353293513 0.2480291233057104 chr4 191154276 10329599 0.05403802214709547 0.27089408007562227 chr5 180915260 9062848 0.0500944364781611 0.25164050004546823 chr6 171115067 8501945 0.04968554288676403 0.31917768307044464 chr7 159138663 7351448 0.04619523540926066 0.36050182391585317 chr8 146364022 8228622 0.05622025062962536 0.49214441775794643 chr9 141213431 6017636 0.04261376525863181 0.3387375928960072 chr10 135534747 6336156 0.0467493107136578 0.3336860329801806 chr11 135006516 6589595 0.04880945894492974 0.3435795140065701 chr12 133851895 6405035 0.047851657236529975 0.2472888412184838 chr13 115169878 4673413 0.040578431454099485 0.22419573892397288 chr14 107349540 4175798 0.03889907679157265 0.23575086355302569 chr15 102531392 3654551 0.03564323987720756 0.21312439560232543 chr16 90354753 3957456 0.04379909045847317 0.2680017735476175 chr17 81195210 3289544 0.04051401554352775 0.25976118192312525 chr18 78077248 3904960 0.050014057872531575 0.5991158235734794 chr19 59128983 2497272 0.04223431341614653 0.5146336596457387 chr20 63025520 2766454 0.04389418762431472 0.24027222499539394 chr21 48129895 2057799 0.04275511093469039 0.24382108739197852 chr22 51304566 1494653 0.029132943060077732 0.18825347452139277 chrMT 16571 4988 0.3010077846840867 0.5979352747937384 chrX 155270560 8187642 0.05273145147412362 0.28296583946864384 chrY 59373566 332384 0.005598181520712433 0.12103712865702063