BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716748.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 = 1,306,671 number of mapped reads = 918,156 (70.27%) number of supplementary alignments = 912 (0.07%) number of secondary alignments = 0 number of mapped bases = 47,602,069 bp number of sequenced bases = 47,590,420 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,525 duplication rate = 7.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2972 >>>>>>> ACTG content number of A's = 10,126,371 bp (21.28%) number of C's = 8,146,446 bp (17.12%) number of T's = 16,122,725 bp (33.88%) number of G's = 13,194,011 bp (27.72%) number of N's = 867 bp (0%) GC percentage = 44.84% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 341,976 number of insertions = 2,778 mapped reads with insertion percentage = 0.3% number of deletions = 6,880 mapped reads with deletion percentage = 0.75% homopolymer indels = 39.32% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1681X There is a 1.31% of reference with a coverageData >= 1X There is a 0.17% 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 4848304 0.01945152224916623 0.197038337599077 chr2 243199373 4300057 0.017681201011977937 0.28983317411341886 chr3 198022430 3393427 0.01713657892189284 0.15084610596369372 chr4 191154276 2621972 0.013716522878096642 0.13964848211896913 chr5 180915260 2896891 0.016012419295088762 0.14634600384855392 chr6 171115067 2093864 0.012236584636933228 0.1501063902504926 chr7 159138663 2640843 0.01659460341199423 0.16612763274860573 chr8 146364022 3040992 0.020776909232516173 0.1720945638739023 chr9 141213431 2179924 0.015437086858968819 0.14831673545366844 chr10 135534747 2377991 0.01754524985389909 0.1723256116153691 chr11 135006516 2091559 0.01549228186882476 0.15515986224933614 chr12 133851895 2326975 0.017384699708584625 0.15441959940890024 chr13 115169878 889217 0.0077209164014222535 0.10376280571811251 chr14 107349540 1534855 0.014297732435555849 0.13889419741248737 chr15 102531392 879335 0.00857625145672459 0.10843215525419503 chr16 90354753 1258939 0.013933290260889762 0.14288530379699574 chr17 81195210 1915303 0.02358886688020143 0.18518396397263656 chr18 78077248 1023910 0.01311406365142378 0.14258358710483784 chr19 59128983 1284221 0.021718976631138743 0.20521724080879483 chr20 63025520 1305467 0.020713307879094055 0.1715914561214998 chr21 48129895 562802 0.011693397627399769 0.13046751848204385 chr22 51304566 501037 0.00976593389368112 0.11626188431336289 chrMT 16571 12745 0.7691147184840987 1.1537625641668028 chrX 155270560 1488286 0.00958511388121483 0.11571760317254307 chrY 59373566 133153 0.002242631005185035 0.07094263468395384