BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 627,396 number of mapped reads = 548,460 (87.42%) number of supplementary alignments = 16,457 (2.62%) number of secondary alignments = 0 number of mapped bases = 72,115,218 bp number of sequenced bases = 70,389,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 476,712 duplication rate = 44.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6085 >>>>>>> ACTG content number of A's = 19,987,153 bp (28.4%) number of C's = 14,663,724 bp (20.83%) number of T's = 19,022,367 bp (27.02%) number of G's = 16,715,546 bp (23.75%) number of N's = 482 bp (0%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.0469 number of mismatches = 3,083,651 number of insertions = 80,626 mapped reads with insertion percentage = 14.16% number of deletions = 280,026 mapped reads with deletion percentage = 47.24% homopolymer indels = 29.92% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 4.3266X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4693168 0.018829112566182936 2.8556337043978433 chr2 243199373 7708161 0.03169482266716206 7.848176037750571 chr3 198022430 4775137 0.024114121819432274 4.759042694042267 chr4 191154276 2590914 0.013554046784702845 1.7587139725462808 chr5 180915260 4075762 0.022528569452902977 4.046750309568097 chr6 171115067 2962380 0.017312210151546735 2.404414721669825 chr7 159138663 3731752 0.023449688024587714 4.262953154822428 chr8 146364022 4003854 0.02735545214793291 5.884049491451899 chr9 141213431 3042298 0.021543970559004404 4.627490295620583 chr10 135534747 4193513 0.030940501183803443 4.3246678501231175 chr11 135006516 3858145 0.028577472512511914 5.016581185517043 chr12 133851895 2680378 0.020024953699758975 2.5712010607485385 chr13 115169878 2436849 0.021158735620089828 3.153435953959119 chr14 107349540 2774284 0.02584346425704293 4.379143877314757 chr15 102531392 1638363 0.01597913544370879 1.8301776225734223 chr16 90354753 1296310 0.014346893295142979 1.6708005941700583 chr17 81195210 1507817 0.018570270339839014 3.2046820770664484 chr18 78077248 2095095 0.026833617393891753 4.032824984124721 chr19 59128983 1114685 0.01885175329330457 2.7503977695352915 chr20 63025520 1512192 0.0239933284168064 5.229365406831476 chr21 48129895 480880 0.009991295430833581 1.2290659728423183 chr22 51304566 629043 0.012260955486885904 2.1652339591245933 chrMT 16571 267769 16.158892040311386 129.9079119462563 chrX 155270560 7660419 0.04933593979438214 5.821041106472652 chrY 59373566 386050 0.006502051771658788 1.7244759046082807