BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716556.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 = 645,740 number of mapped reads = 574,833 (89.02%) number of supplementary alignments = 2,320 (0.36%) number of secondary alignments = 0 number of mapped bases = 32,649,561 bp number of sequenced bases = 32,641,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,427 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9083 >>>>>>> ACTG content number of A's = 7,942,227 bp (24.33%) number of C's = 6,218,180 bp (19.05%) number of T's = 10,347,116 bp (31.7%) number of G's = 8,133,042 bp (24.92%) number of N's = 691 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 154,273 number of insertions = 1,777 mapped reads with insertion percentage = 0.31% number of deletions = 4,931 mapped reads with deletion percentage = 0.85% homopolymer indels = 41.46% >>>>>>> Coverage mean coverageData = 0.0105X std coverageData = 0.1173X There is a 1% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2703937 0.010848265850459005 0.1520676753795272 chr2 243199373 2437799 0.010023870415159335 0.12021417202957538 chr3 198022430 2173774 0.010977413013263194 0.1090870027972707 chr4 191154276 2163561 0.011318402314997129 0.11229201623618741 chr5 180915260 2001453 0.011062930788701849 0.10929756827602181 chr6 171115067 1929139 0.011273928320993498 0.11209161363814747 chr7 159138663 1768859 0.011115205862952362 0.12363989914701769 chr8 146364022 1581741 0.010806897613130636 0.11487635407885831 chr9 141213431 1266980 0.008972092746616998 0.11074319091086463 chr10 135534747 1480529 0.010923612083032847 0.11632698640973373 chr11 135006516 1496788 0.011086783396439917 0.11874210909273478 chr12 133851895 1496170 0.011177802152147342 0.10996263902792099 chr13 115169878 905979 0.007866457929216527 0.0916286660286786 chr14 107349540 1030456 0.009599072338828838 0.10228750320734054 chr15 102531392 989833 0.009653950665177744 0.10184159242081096 chr16 90354753 973659 0.01077595774070679 0.1100950060594164 chr17 81195210 952488 0.011730839787223902 0.11482759167600774 chr18 78077248 872125 0.011170027406703678 0.163958803729185 chr19 59128983 738954 0.01249732301331819 0.1366547212290756 chr20 63025520 718374 0.011398144751522876 0.11091003796167252 chr21 48129895 449955 0.00934876338292448 0.10318281445000295 chr22 51304566 415486 0.008098421493322835 0.09351827039541295 chrMT 16571 6539 0.3946050328887816 0.6510867279705088 chrX 155270560 2002778 0.012898633198720994 0.12292808231235579 chrY 59373566 92205 0.0015529638223178309 0.04722856136817254