BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237574.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 = 2,239,385 number of mapped reads = 1,890,504 (84.42%) number of supplementary alignments = 14,447 (0.65%) number of secondary alignments = 0 number of mapped bases = 118,204,793 bp number of sequenced bases = 118,136,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,084 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3032 >>>>>>> ACTG content number of A's = 32,545,174 bp (27.55%) number of C's = 20,385,750 bp (17.26%) number of T's = 38,215,479 bp (32.35%) number of G's = 26,776,690 bp (22.67%) number of N's = 213,085 bp (0.18%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,080,797 number of insertions = 10,075 mapped reads with insertion percentage = 0.53% number of deletions = 42,086 mapped reads with deletion percentage = 2.2% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.3504X There is a 3.22% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% 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 10748165 0.043121918641077325 0.5938558160188676 chr2 243199373 10531576 0.043304289275449735 0.4172621531518801 chr3 198022430 8478758 0.04281715965206568 0.24065910189645856 chr4 191154276 6165554 0.0322543347133914 0.22554575112091854 chr5 180915260 6980753 0.03858576109057909 0.22706921086571272 chr6 171115067 7417520 0.043348140698796556 0.2752088397885061 chr7 159138663 6765171 0.042511171530955995 0.4340169489966302 chr8 146364022 6643580 0.045390799659768846 0.6119844314422944 chr9 141213431 5116691 0.03623374181737713 0.3106295261842667 chr10 135534747 5691651 0.04199403566968698 0.32234824331563317 chr11 135006516 5543454 0.04106064036198075 0.29204447319395804 chr12 133851895 5643321 0.04216093466588575 0.24479558835320991 chr13 115169878 3967964 0.034453140603309486 0.21590268035474694 chr14 107349540 3325114 0.03097464600220923 0.2218648226144914 chr15 102531392 2585807 0.02521966150620485 0.18703694470418544 chr16 90354753 2737859 0.030301217247530963 0.22158257381456853 chr17 81195210 2872232 0.0353744020121384 0.2322820124748601 chr18 78077248 2667509 0.03416499772123116 0.5114883391272437 chr19 59128983 1843253 0.031173426405794936 0.42611038384781247 chr20 63025520 2261915 0.03588887485577271 0.22565054173922486 chr21 48129895 1549706 0.032198408078804246 0.22209005974845558 chr22 51304566 1134739 0.02211770001134012 0.16886315835523924 chrMT 16571 110327 6.657835978516686 4.558548346265613 chrX 155270560 7082141 0.04561161497710835 0.2658407690747506 chrY 59373566 340033 0.005727009895278986 0.12693571182087324