BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084847.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 = 2,521,349 number of mapped reads = 2,186,574 (86.72%) number of supplementary alignments = 18,570 (0.74%) number of secondary alignments = 0 number of mapped bases = 150,920,572 bp number of sequenced bases = 150,862,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,941 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0382 >>>>>>> ACTG content number of A's = 43,833,478 bp (29.06%) number of C's = 27,711,727 bp (18.37%) number of T's = 48,316,124 bp (32.03%) number of G's = 30,977,234 bp (20.53%) number of N's = 24,098 bp (0.02%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,227,377 number of insertions = 12,005 mapped reads with insertion percentage = 0.54% number of deletions = 32,217 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.3815X There is a 3.95% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 11828387 0.04745579751233599 0.5373658253689507 chr2 243199373 13281350 0.054610954938605044 0.35807523479736086 chr3 198022430 10214383 0.05158194958015615 0.2687878978303031 chr4 191154276 10316422 0.05396908829808233 0.28543669144490363 chr5 180915260 9926428 0.05486783149193716 0.2774707206051573 chr6 171115067 9152339 0.053486458910132095 0.2841466347667172 chr7 159138663 8312702 0.052235590291468015 0.3039214822873355 chr8 146364022 8037417 0.05491388450639871 0.9385134466024315 chr9 141213431 6324791 0.04478887705801865 0.32160909251534703 chr10 135534747 6909607 0.05098033642988982 0.34506879823382525 chr11 135006516 6760115 0.05007250909282038 0.29492556093938177 chr12 133851895 6837515 0.05108269105939815 0.26813500081027913 chr13 115169878 4969024 0.04314517030225559 0.246752336440248 chr14 107349540 4601473 0.04286439420234125 0.25560135265080614 chr15 102531392 4233353 0.041288359764002816 0.24053161059933767 chr16 90354753 3528901 0.03905606382433473 0.24753366205900204 chr17 81195210 3471634 0.042756635520740695 0.26537886443240216 chr18 78077248 4141396 0.05304228960528937 0.5705428840237695 chr19 59128983 2179226 0.03685546223583788 0.35432495377235296 chr20 63025520 2958869 0.046947157278511946 0.26278051128274266 chr21 48129895 1916915 0.03982794892862326 0.2508062479639311 chr22 51304566 1297819 0.02529636446003656 0.1845822622247646 chrMT 16571 278652 16.815641783839236 8.431766284831573 chrX 155270560 9072138 0.05842793379504782 0.2953188565783096 chrY 59373566 369716 0.0062269461800559525 0.14870728391644977