BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231813.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 = 4,992,831 number of mapped reads = 4,669,154 (93.52%) number of supplementary alignments = 33,322 (0.67%) number of secondary alignments = 0 number of mapped bases = 300,638,970 bp number of sequenced bases = 300,524,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 526,225 duplication rate = 9.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.982 >>>>>>> ACTG content number of A's = 79,079,651 bp (26.31%) number of C's = 53,560,222 bp (17.82%) number of T's = 98,632,332 bp (32.82%) number of G's = 69,136,189 bp (23.01%) number of N's = 116,289 bp (0.04%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,873,658 number of insertions = 19,742 mapped reads with insertion percentage = 0.42% number of deletions = 65,296 mapped reads with deletion percentage = 1.38% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.0971X std coverageData = 0.959X There is a 7.25% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 25958958 0.10414801734837002 1.9743545400503724 chr2 243199373 21096422 0.08674537989043253 1.45726068817701 chr3 198022430 24479454 0.12361960208245096 0.45069920942880914 chr4 191154276 15919407 0.0832804127279894 0.4070394082483809 chr5 180915260 18259678 0.10092945172231463 0.41986210508831023 chr6 171115067 24791024 0.14487925835309406 0.750544415349964 chr7 159138663 21154578 0.1329317313668772 1.449962906048405 chr8 146364022 16581642 0.11329042324349355 1.2490122512954687 chr9 141213431 9411998 0.06665086977456132 0.6171283787022105 chr10 135534747 12532919 0.0924701545353532 0.6714367400035745 chr11 135006516 10996074 0.08144846875390814 0.5557037038818913 chr12 133851895 10777192 0.08051579695603114 0.38321672269052337 chr13 115169878 9096649 0.07898461957214195 0.402969374698154 chr14 107349540 11113853 0.10352958196187892 0.44193734197294954 chr15 102531392 8695270 0.08480592948547895 0.40972982114977907 chr16 90354753 8315419 0.09203078669253846 0.4452813404472434 chr17 81195210 8047440 0.09911225058719597 0.4648995650900676 chr18 78077248 8729392 0.11180455540646105 1.4428148553151687 chr19 59128983 8128001 0.13746221544179105 1.1128698404486919 chr20 63025520 7046931 0.1118107553892455 0.4523969429241534 chr21 48129895 6721045 0.13964387414516488 0.510957898682795 chr22 51304566 2586285 0.05041042545803818 0.2769009106764976 chrMT 16571 635776 38.36678534789693 20.390155666536913 chrX 155270560 8861894 0.057073884450471485 0.39889520914825144 chrY 59373566 701669 0.01181786857808069 0.2672078416375753