BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080971.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,900,942 number of mapped reads = 6,112,071 (88.57%) number of supplementary alignments = 63,087 (0.91%) number of secondary alignments = 0 number of mapped bases = 411,071,128 bp number of sequenced bases = 410,920,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 500,298 duplication rate = 6.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0347 >>>>>>> ACTG content number of A's = 115,520,108 bp (28.11%) number of C's = 72,379,485 bp (17.61%) number of T's = 133,834,754 bp (32.57%) number of G's = 88,373,943 bp (21.51%) number of N's = 811,763 bp (0.2%) GC percentage = 39.12% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 4,077,421 number of insertions = 32,332 mapped reads with insertion percentage = 0.53% number of deletions = 91,362 mapped reads with deletion percentage = 1.48% homopolymer indels = 49.22% >>>>>>> Coverage mean coverageData = 0.1328X std coverageData = 0.8357X There is a 8.55% of reference with a coverageData >= 1X There is a 2.85% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 34187355 0.13716056097609483 1.1218477725455038 chr2 243199373 26978328 0.1109309109937549 0.7880233224995569 chr3 198022430 35957079 0.1815808390998939 0.6110101789106913 chr4 191154276 26208982 0.13710905425939832 0.5558091110149128 chr5 180915260 23927419 0.13225760502458445 0.5160025011396568 chr6 171115067 35483115 0.20736405988141302 0.9662177127925633 chr7 159138663 20163862 0.12670624234162378 0.8296461594742336 chr8 146364022 32079926 0.21917904114441458 1.683333906300064 chr9 141213431 20128172 0.14253723500280932 1.0156238048274393 chr10 135534747 18467090 0.13625354684876492 0.7035707849880766 chr11 135006516 18312721 0.13564323813822438 0.6826139354198026 chr12 133851895 20205287 0.1509525658938187 0.5804495336296757 chr13 115169878 11218673 0.09740978452716603 0.44118240351696475 chr14 107349540 11490437 0.10703759885696762 0.5961098666919359 chr15 102531392 10375197 0.10119044321567389 0.45283592580463955 chr16 90354753 9687410 0.10721527842591745 0.5807988055693353 chr17 81195210 7977274 0.0982480863095249 0.4670380471101958 chr18 78077248 10316813 0.1321359712883323 1.7733794951155266 chr19 59128983 7371878 0.12467452721113097 0.8951086245848965 chr20 63025520 6536078 0.10370526097999667 0.4880231376699071 chr21 48129895 7606323 0.158037390274797 0.6902584744748212 chr22 51304566 3229823 0.06295390940447679 0.34626630878391085 chrMT 16571 202494 12.219781546074467 6.783612267069825 chrX 155270560 12071019 0.07774183979242427 0.45647170864524284 chrY 59373566 888373 0.014962432945327892 0.2691504402139688