BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717080.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 = 887,540 number of mapped reads = 796,522 (89.74%) number of supplementary alignments = 1,816 (0.2%) number of secondary alignments = 0 number of mapped bases = 45,904,018 bp number of sequenced bases = 45,889,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,008 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5678 >>>>>>> ACTG content number of A's = 11,150,830 bp (24.3%) number of C's = 8,460,121 bp (18.44%) number of T's = 14,919,333 bp (32.51%) number of G's = 11,359,121 bp (24.75%) number of N's = 525 bp (0%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 224,544 number of insertions = 3,458 mapped reads with insertion percentage = 0.43% number of deletions = 9,030 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.94% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1538X There is a 1.39% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 5477656 0.02197649890709801 0.20781837438534656 chr2 243199373 4741591 0.01949672378472785 0.2165124840950598 chr3 198022430 2944914 0.014871618331317315 0.13121242971129798 chr4 191154276 1949777 0.010200017707163401 0.10848574607589376 chr5 180915260 3231687 0.0178629873455672 0.14013876913295945 chr6 171115067 1753938 0.010250050043810579 0.11609684958514385 chr7 159138663 2457802 0.015444405235451802 0.1930551872044462 chr8 146364022 2099445 0.014343996368178513 0.13957922793871122 chr9 141213431 1316420 0.009322201087232276 0.12365560059144413 chr10 135534747 2137229 0.015768864053732286 0.17626903539554425 chr11 135006516 2245223 0.01663047878370552 0.15568453017451864 chr12 133851895 1866198 0.01394226058585125 0.12425879873944333 chr13 115169878 1308818 0.011364238833351895 0.11150814080885255 chr14 107349540 976458 0.00909606133384456 0.10234960266661189 chr15 102531392 1902963 0.018559808492602928 0.14336007009189075 chr16 90354753 1385440 0.015333338357972159 0.13834879207668968 chr17 81195210 1723369 0.021225008224007302 0.15906856797215158 chr18 78077248 1517165 0.01943158908469725 0.2258984046633706 chr19 59128983 713456 0.012066096249279309 0.16205233176186476 chr20 63025520 1183951 0.018785263493264315 0.14372479813536146 chr21 48129895 597231 0.012408732659815692 0.11885389805813681 chr22 51304566 508000 0.00990165280805611 0.10396899467799502 chrMT 16571 3160 0.1906945869289723 0.46515185540331405 chrX 155270560 1756366 0.011311648518560119 0.12187891043777836 chrY 59373566 105761 0.0017812809154834999 0.05277349861504915