BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716782.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 = 2,426,397 number of mapped reads = 2,102,561 (86.65%) number of supplementary alignments = 53,277 (2.2%) number of secondary alignments = 0 number of mapped bases = 157,995,340 bp number of sequenced bases = 157,939,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,530 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1939 >>>>>>> ACTG content number of A's = 41,314,549 bp (26.16%) number of C's = 31,513,265 bp (19.95%) number of T's = 48,117,035 bp (30.47%) number of G's = 36,975,297 bp (23.41%) number of N's = 19,283 bp (0.01%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,168,103 number of insertions = 14,582 mapped reads with insertion percentage = 0.69% number of deletions = 32,576 mapped reads with deletion percentage = 1.53% homopolymer indels = 39.76% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.4126X There is a 4.31% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 12987002 0.05210419114662908 0.48615915091824186 chr2 243199373 13866630 0.05701754009045081 0.6207973503309752 chr3 198022430 10676027 0.05391322084068961 0.2660217084798053 chr4 191154276 10049434 0.0525723735314192 0.2879122616685896 chr5 180915260 9821889 0.05428999742752491 0.27243569760475417 chr6 171115067 9461364 0.05529240741845369 0.3160143923958018 chr7 159138663 9057375 0.05691498740315545 0.5342281738908073 chr8 146364022 8482334 0.05795368208725502 0.522543996656343 chr9 141213431 6764522 0.04790282306787093 0.44585258744258555 chr10 135534747 7465606 0.0550825981178096 0.41478094328672704 chr11 135006516 7394813 0.054773748846314946 0.465906326643548 chr12 133851895 7534405 0.056289117161919894 0.2772866166498058 chr13 115169878 5178243 0.044961782454957536 0.2408256293550056 chr14 107349540 4790727 0.04462736402969216 0.2988087081062852 chr15 102531392 4606935 0.04493194630577141 0.24601789308313346 chr16 90354753 4816492 0.053306459705556385 0.3032864210506114 chr17 81195210 4385342 0.0540098609265251 0.2975408745748771 chr18 78077248 4584670 0.05871966696367167 0.8852033476341463 chr19 59128983 3211632 0.05431569827608907 0.4214217485734982 chr20 63025520 3416535 0.05420875543747993 0.28784227182368266 chr21 48129895 2156663 0.04480921888568425 0.268193521719622 chr22 51304566 1785228 0.03479666897484329 0.21359064161678892 chrMT 16571 17369 1.0481564178383924 1.2675576996571356 chrX 155270560 5128531 0.0330296419359858 0.30432835599548874 chrY 59373566 355572 0.00598872568981287 0.19816232912662093