BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716468.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 = 621,326 number of mapped reads = 465,276 (74.88%) number of supplementary alignments = 2,160 (0.35%) number of secondary alignments = 0 number of mapped bases = 27,651,583 bp number of sequenced bases = 27,643,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,896 duplication rate = 0.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9559 >>>>>>> ACTG content number of A's = 7,559,154 bp (27.35%) number of C's = 5,106,090 bp (18.47%) number of T's = 8,368,078 bp (30.27%) number of G's = 6,609,723 bp (23.91%) number of N's = 173 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 135,695 number of insertions = 2,441 mapped reads with insertion percentage = 0.52% number of deletions = 5,164 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.42% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.1119X There is a 0.86% of reference with a coverageData >= 1X There is a 0.02% 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 3311177 0.013284528586991966 0.17290991852632018 chr2 243199373 2900752 0.011927464961021919 0.13353440351396173 chr3 198022430 1809046 0.009135561057401426 0.09838201454927097 chr4 191154276 1168995 0.006115453049033546 0.08113055234369757 chr5 180915260 2056069 0.011364817981634053 0.10925059929488684 chr6 171115067 1055233 0.006166803534606336 0.08415383978804142 chr7 159138663 1447957 0.009098712862756677 0.1299299608704648 chr8 146364022 1250882 0.008546376239920491 0.10227066530079383 chr9 141213431 753937 0.005338989320357212 0.08821149907386591 chr10 135534747 1256498 0.009270670642119545 0.11113637313808544 chr11 135006516 1208584 0.008952041988847413 0.11030592062081991 chr12 133851895 1134728 0.008477489242868022 0.09436696687702671 chr13 115169878 835812 0.007257210084046456 0.08708415795048288 chr14 107349540 606297 0.005647877019314661 0.07749107272646873 chr15 102531392 1206866 0.01177069750501388 0.11146218690054066 chr16 90354753 822095 0.009098525231981985 0.10059752042973168 chr17 81195210 1006310 0.012393711402433715 0.11692666963260111 chr18 78077248 920591 0.01179077162145879 0.16105146515405808 chr19 59128983 416654 0.007046527419556667 0.13137616530250168 chr20 63025520 716346 0.011365967309750083 0.10910648611787786 chr21 48129895 350323 0.007278698613408569 0.08807084237829774 chr22 51304566 310365 0.006049461562543965 0.079404261883642 chrMT 16571 3078 0.185746183090942 0.45245811612077375 chrX 155270560 1046054 0.0067369757666875165 0.08866290525523726 chrY 59373566 56934 9.589115802813663E-4 0.035076870207467664