BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716892.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 = 4,728,570 number of mapped reads = 4,224,177 (89.33%) number of supplementary alignments = 99,100 (2.1%) number of secondary alignments = 0 number of mapped bases = 315,735,818 bp number of sequenced bases = 315,624,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,014 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1488 >>>>>>> ACTG content number of A's = 80,828,508 bp (25.61%) number of C's = 66,361,914 bp (21.03%) number of T's = 95,237,944 bp (30.17%) number of G's = 73,158,389 bp (23.18%) number of N's = 37,967 bp (0.01%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,280,277 number of insertions = 28,576 mapped reads with insertion percentage = 0.67% number of deletions = 65,618 mapped reads with deletion percentage = 1.53% homopolymer indels = 39.96% >>>>>>> Coverage mean coverageData = 0.102X std coverageData = 0.7159X There is a 7.78% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 25036102 0.10044549497832544 0.8446064130053829 chr2 243199373 26879659 0.11052519859909343 1.1154401164026022 chr3 198022430 21228302 0.10720150237526123 0.40987514009321024 chr4 191154276 20071058 0.1049992624805317 0.46826970104911747 chr5 180915260 18883019 0.10437493774709773 0.4127727213289552 chr6 171115067 18280249 0.10683015423767446 0.5145606908909666 chr7 159138663 17371380 0.10915876552261847 0.9315955217043967 chr8 146364022 16198222 0.11067079039410382 0.9667258727458365 chr9 141213431 13438344 0.09516335595585097 0.7882058125954976 chr10 135534747 15123554 0.11158433047431003 0.7066730630722257 chr11 135006516 14286310 0.10581941096828244 0.8011921017088057 chr12 133851895 14176624 0.10591276275916751 0.4203450365298527 chr13 115169878 9974203 0.08660426817505182 0.36688470573087334 chr14 107349540 9532163 0.08879556447097957 0.5039416850708076 chr15 102531392 9184626 0.08957867264690994 0.3792621209924187 chr16 90354753 9315213 0.10309599319030843 0.4891591711404321 chr17 81195210 8672503 0.10681052490658008 0.4858237662466369 chr18 78077248 8735617 0.11188428413870324 1.5487161830782754 chr19 59128983 6456042 0.10918574398615988 0.754841667932745 chr20 63025520 6758018 0.10722669166394819 0.445451600327713 chr21 48129895 4187799 0.08701034980441989 0.43143998578576737 chr22 51304566 3662629 0.07138992268251523 0.33798991091698105 chrMT 16571 10638 0.6419648784020276 1.6863701835054947 chrX 155270560 17471858 0.11252524625402266 0.6212553322737662 chrY 59373566 801686 0.01350240610442701 0.34565462208877484