BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,697,652 number of mapped reads = 2,395,140 (88.79%) number of supplementary alignments = 20,992 (0.78%) number of secondary alignments = 0 number of mapped bases = 159,401,081 bp number of sequenced bases = 159,333,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,815 duplication rate = 7.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.188 >>>>>>> ACTG content number of A's = 44,229,769 bp (27.76%) number of C's = 28,642,266 bp (17.98%) number of T's = 51,220,516 bp (32.15%) number of G's = 35,064,307 bp (22.01%) number of N's = 176,452 bp (0.11%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,413,263 number of insertions = 11,924 mapped reads with insertion percentage = 0.49% number of deletions = 41,070 mapped reads with deletion percentage = 1.7% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.0515X std coverageData = 0.7204X There is a 3.34% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% 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% 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 42575688 0.17081477201214276 1.7181607788369664 chr2 243199373 4890723 0.020109932602498937 0.7102645486117947 chr3 198022430 3094822 0.01562864368445534 0.285358191246406 chr4 191154276 15116662 0.07908095134633557 0.4119723297715457 chr5 180915260 4486272 0.024797642830129422 0.22189342283535116 chr6 171115067 12679644 0.07410010247665684 0.5785509882881289 chr7 159138663 5674833 0.035659674984199155 0.7102078042268014 chr8 146364022 5429675 0.03709706064240295 0.9862156932779763 chr9 141213431 3180075 0.02251963554373238 0.46540209167447205 chr10 135534747 10713431 0.0790456413365349 1.1121131783423415 chr11 135006516 2111534 0.0156402376904534 0.25328829469125425 chr12 133851895 7225739 0.053983090788516666 0.34473151528733853 chr13 115169878 2073735 0.018005879974970537 0.19080672265093243 chr14 107349540 2751933 0.025635256564676478 0.24900014163418607 chr15 102531392 2292981 0.022363697159207593 0.20925587613768268 chr16 90354753 5395806 0.059718009521867656 0.37564625648321964 chr17 81195210 6284441 0.07739915938390947 0.42971964223813164 chr18 78077248 5708106 0.07310844255166371 0.7429491782608977 chr19 59128983 2167123 0.036650774122057875 0.9644855601491585 chr20 63025520 3693442 0.058602324899501027 0.3475667366979532 chr21 48129895 967188 0.020095369000908893 0.2087468479019124 chr22 51304566 4754030 0.09266290255724997 0.4282305927291648 chrMT 16571 284950 17.195703337155273 9.750367868289484 chrX 155270560 5212247 0.033568804028271684 0.2980216172868018 chrY 59373566 636001 0.010711854497673258 0.1815138986664954