BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716667.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 = 2,611,774 number of mapped reads = 2,427,422 (92.94%) number of supplementary alignments = 44,048 (1.69%) number of secondary alignments = 0 number of mapped bases = 192,815,464 bp number of sequenced bases = 192,724,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,735 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5697 >>>>>>> ACTG content number of A's = 50,293,574 bp (26.1%) number of C's = 38,525,704 bp (19.99%) number of T's = 58,347,297 bp (30.27%) number of G's = 45,544,833 bp (23.63%) number of N's = 13,534 bp (0.01%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,285,334 number of insertions = 15,841 mapped reads with insertion percentage = 0.64% number of deletions = 46,743 mapped reads with deletion percentage = 1.9% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0623X std coverageData = 0.5452X There is a 5.07% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18782994 0.0753578623982646 1.1075012399401634 chr2 243199373 15494834 0.06371247511398806 0.608530331703135 chr3 198022430 12263398 0.06192933800479067 0.2885100384588148 chr4 191154276 12184088 0.06373955244401648 0.406630303920656 chr5 180915260 10915777 0.060336408327301964 0.28940342298299293 chr6 171115067 10721867 0.06265881308979063 0.3251941603274252 chr7 159138663 10144660 0.06374729942276817 0.672432111376938 chr8 146364022 9406814 0.06426998842652738 0.6330334667853664 chr9 141213431 7892983 0.055893996372058975 0.4528302844729811 chr10 135534747 8891314 0.0656017308978339 0.527496392675022 chr11 135006516 10979800 0.08132792642393645 0.6363985816554553 chr12 133851895 8456649 0.06317915035868563 0.29680066523454607 chr13 115169878 6717721 0.05832880191120807 0.28386086579607306 chr14 107349540 5644223 0.05257798962156708 0.299252347560985 chr15 102531392 5475154 0.05339978218573293 0.2695809223842136 chr16 90354753 4367519 0.048337457134103395 0.29896574282347843 chr17 81195210 6203171 0.07639823827045955 0.41644728540761544 chr18 78077248 5024204 0.06434914304356629 0.7868464202189853 chr19 59128983 3476912 0.0588021613698311 0.8186643494557124 chr20 63025520 3859187 0.06123213263452646 0.3124052348746162 chr21 48129895 2567339 0.053341878265057506 0.3294472249024033 chr22 51304566 2298346 0.04479807898579631 0.25028496016935237 chrMT 16571 79378 4.790175607989862 3.3397760979084445 chrX 155270560 10383460 0.06687333387604193 0.3743256733834981 chrY 59373566 583672 0.009830502685319592 0.3108967128931341