BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716460.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 = 1,395,338 number of mapped reads = 1,264,878 (90.65%) number of supplementary alignments = 4,368 (0.31%) number of secondary alignments = 0 number of mapped bases = 73,702,573 bp number of sequenced bases = 73,680,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,852 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4108 >>>>>>> ACTG content number of A's = 18,345,924 bp (24.9%) number of C's = 13,840,133 bp (18.78%) number of T's = 22,471,406 bp (30.5%) number of G's = 19,021,929 bp (25.82%) number of N's = 676 bp (0%) GC percentage = 44.6% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 382,696 number of insertions = 4,385 mapped reads with insertion percentage = 0.34% number of deletions = 14,046 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.26% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.207X There is a 2.16% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 5913433 0.023724847610309463 0.2532881207196094 chr2 243199373 6150518 0.025290024082422286 0.28096466555324145 chr3 198022430 4888945 0.024688844591998996 0.17110339590463933 chr4 191154276 4751539 0.024857089778101537 0.193528961151708 chr5 180915260 4373043 0.024171775227805548 0.16728712932972586 chr6 171115067 4192156 0.024499046597690897 0.18709417101899975 chr7 159138663 4026385 0.025301111144813374 0.25368888749970253 chr8 146364022 3663984 0.025033365098425624 0.20625316579537642 chr9 141213431 3140557 0.022239789641539127 0.18213879025907231 chr10 135534747 3568481 0.026328901473509223 0.2706960304021991 chr11 135006516 3325865 0.024634847995040475 0.1944015445837848 chr12 133851895 3389474 0.02532257014366513 0.17328233135867055 chr13 115169878 2265733 0.019672965182788507 0.15073292198141278 chr14 107349540 2224027 0.02071762021523334 0.16134300263842904 chr15 102531392 2146999 0.020939918576351718 0.15757917067421637 chr16 90354753 2228925 0.02466859712404947 0.18404956966022384 chr17 81195210 2117377 0.026077609750624453 0.1802522066858819 chr18 78077248 1925514 0.024661653033672497 0.26108717326657144 chr19 59128983 1607545 0.027187090297155964 0.23590331665278164 chr20 63025520 1583334 0.025122109266214703 0.1777362191434167 chr21 48129895 947668 0.019689799863473627 0.1696520868810454 chr22 51304566 916108 0.017856266438351705 0.14639523443231767 chrMT 16571 6312 0.3809064027517953 0.6181789258375427 chrX 155270560 4102645 0.02642255557009648 0.18525779549203894 chrY 59373566 246006 0.004143359016030804 0.1390700878052839