BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,766,639 number of mapped reads = 2,229,122 (80.57%) number of supplementary alignments = 7,381 (0.27%) number of secondary alignments = 0 number of mapped bases = 132,720,711 bp number of sequenced bases = 132,647,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 731,075 duplication rate = 17.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2434 >>>>>>> ACTG content number of A's = 34,020,796 bp (25.65%) number of C's = 21,957,472 bp (16.55%) number of T's = 44,283,481 bp (33.38%) number of G's = 32,303,807 bp (24.35%) number of N's = 82,079 bp (0.06%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,311,302 number of insertions = 9,109 mapped reads with insertion percentage = 0.41% number of deletions = 42,482 mapped reads with deletion percentage = 1.89% homopolymer indels = 49.78% >>>>>>> Coverage mean coverageData = 0.0429X std coverageData = 0.6468X There is a 1.64% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 9207648 0.03694132421038181 0.707287731797312 chr2 243199373 14356240 0.05903074429390079 0.7666623789991478 chr3 198022430 9938770 0.05019012240179054 0.5749408715632937 chr4 191154276 9733213 0.05091810240227114 0.5892641114712014 chr5 180915260 6548955 0.03619901936409344 0.4716430699896216 chr6 171115067 9243352 0.05401834076948934 0.6364142717907748 chr7 159138663 8178316 0.05139113177041082 1.3615694134991063 chr8 146364022 8666049 0.05920887443226997 0.7511872930984794 chr9 141213431 5086068 0.03601688567428123 0.5379696766406789 chr10 135534747 4633603 0.0341875652005312 0.501236941626726 chr11 135006516 4503530 0.03335787140822151 0.4781233952230444 chr12 133851895 6321676 0.047228886823006876 0.555470740578501 chr13 115169878 3221230 0.027969379285093972 0.41948116210458336 chr14 107349540 4793447 0.04465270181875022 0.5454037421889351 chr15 102531392 2623630 0.02558855340616072 0.4265459282885639 chr16 90354753 3341237 0.03697909505657107 0.47698993519775434 chr17 81195210 3464085 0.0426636620559267 0.5237855957847899 chr18 78077248 3563655 0.04564268197567619 0.7441675854403765 chr19 59128983 2166997 0.03664864318738579 0.5849424517585086 chr20 63025520 2104933 0.03339810603704658 0.4383430306378545 chr21 48129895 2374365 0.04933243673188981 0.5633543615245351 chr22 51304566 1255627 0.024473981516576905 0.36895687795089804 chrMT 16571 46002 2.776054553134995 4.6075158789398225 chrX 155270560 7067197 0.045515370074017895 0.5544769862692785 chrY 59373566 280886 0.00473082583586103 0.13512723744892566