BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716696.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,122,658 number of mapped reads = 1,029,633 (91.71%) number of supplementary alignments = 16,240 (1.45%) number of secondary alignments = 0 number of mapped bases = 80,541,181 bp number of sequenced bases = 80,506,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,972 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8879 >>>>>>> ACTG content number of A's = 20,343,995 bp (25.27%) number of C's = 16,423,916 bp (20.4%) number of T's = 24,221,512 bp (30.09%) number of G's = 19,512,348 bp (24.24%) number of N's = 4,832 bp (0.01%) GC percentage = 44.64% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 668,936 number of insertions = 7,929 mapped reads with insertion percentage = 0.76% number of deletions = 19,652 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 0.344X There is a 2.31% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7817142 0.031362577828843205 0.5492089339000824 chr2 243199373 7038507 0.02894130405508899 0.5999368048760962 chr3 198022430 5936762 0.029980250217109244 0.1954168091591378 chr4 191154276 3164110 0.016552650906956432 0.1593487148130895 chr5 180915260 5207297 0.028783072251616585 0.1858311805523762 chr6 171115067 5176149 0.030249522094977176 0.23640077806778492 chr7 159138663 4337611 0.0272568018244567 0.45530968658072224 chr8 146364022 5323884 0.03637426689463344 0.45753968995952016 chr9 141213431 4280552 0.030312640728911967 0.33425272604084316 chr10 135534747 4362012 0.03218371743446719 0.4300404312849011 chr11 135006516 3030224 0.022445020357387786 0.23665658583464205 chr12 133851895 3245580 0.02424754614045621 0.17338728302612727 chr13 115169878 1909627 0.016580958781600864 0.14009639735471643 chr14 107349540 1941719 0.018087818541187975 0.16438076594458587 chr15 102531392 1920669 0.018732497067824847 0.15347472334611892 chr16 90354753 2162175 0.02392984240685158 0.18688613468767903 chr17 81195210 2792463 0.03439196721087365 0.23244320079921643 chr18 78077248 1893421 0.02425061139449997 0.5053117923264094 chr19 59128983 1751686 0.029624828825484787 0.4458167581032877 chr20 63025520 1364637 0.02165213392924009 0.17068662574095309 chr21 48129895 1192326 0.02477308541811695 0.178848710511491 chr22 51304566 1042518 0.020320179689269764 0.155288345282945 chrMT 16571 35132 2.1200893126546374 2.2231752899620076 chrX 155270560 3393718 0.021856802731953822 0.20344152933923468 chrY 59373566 221260 0.0037265742131776286 0.1366299247522197