BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080903.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 = 4,014,087 number of mapped reads = 3,628,467 (90.39%) number of supplementary alignments = 37,219 (0.93%) number of secondary alignments = 0 number of mapped bases = 248,233,904 bp number of sequenced bases = 248,143,532 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,478 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.03 >>>>>>> ACTG content number of A's = 71,434,466 bp (28.79%) number of C's = 43,528,362 bp (17.54%) number of T's = 80,237,866 bp (32.34%) number of G's = 51,749,516 bp (20.85%) number of N's = 1,193,322 bp (0.48%) GC percentage = 38.4% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 2,840,758 number of insertions = 18,759 mapped reads with insertion percentage = 0.51% number of deletions = 54,974 mapped reads with deletion percentage = 1.5% homopolymer indels = 49.93% >>>>>>> Coverage mean coverageData = 0.0802X std coverageData = 0.5148X There is a 5.69% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19178606 0.07694506807266892 0.7094302439754293 chr2 243199373 21387437 0.08794199070570795 0.5031220217898495 chr3 198022430 17776459 0.08976992656841955 0.3996435047497179 chr4 191154276 17695404 0.09257132181547433 0.4158020116929491 chr5 180915260 15918178 0.0879869282447484 0.39558294322443066 chr6 171115067 15385861 0.08991529074409327 0.504920316738715 chr7 159138663 13483324 0.08472689003300223 0.6018682287315616 chr8 146364022 13129964 0.08970759221142474 1.0237834521567712 chr9 141213431 10404619 0.0736800949195831 0.4747696256253573 chr10 135534747 10966821 0.08091519881613828 0.44965216157607657 chr11 135006516 11146242 0.08256077062236018 0.4425826447439086 chr12 133851895 11231357 0.08390883819762134 0.3883308866103006 chr13 115169878 8872012 0.07703413560966002 0.3706125098357399 chr14 107349540 7475556 0.06963752243372445 0.36748597880188655 chr15 102531392 6552486 0.06390712027005349 0.3357512675937918 chr16 90354753 6104066 0.06755666743950924 0.36511711375590034 chr17 81195210 5484898 0.06755198982797138 0.3733045237306698 chr18 78077248 6963434 0.08918646825256955 0.7732243332561005 chr19 59128983 3448100 0.05831488764148032 0.5170791043159468 chr20 63025520 4451459 0.07062946882469197 0.36598104942425086 chr21 48129895 3346238 0.06952514648120467 0.37302604733990513 chr22 51304566 2166055 0.04221953656132672 0.26998713989464385 chrMT 16571 116969 7.058656689397139 4.184454940802056 chrX 155270560 15029170 0.09679342948206021 0.4403907203641957 chrY 59373566 519189 0.008744446981675313 0.15562422711308138