BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818877.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,960,410 number of mapped reads = 1,909,222 (97.39%) number of supplementary alignments = 28,420 (1.45%) number of secondary alignments = 0 number of mapped bases = 176,830,469 bp number of sequenced bases = 176,717,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 428,974 duplication rate = 19.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0831 >>>>>>> ACTG content number of A's = 49,714,412 bp (28.13%) number of C's = 37,822,398 bp (21.4%) number of T's = 52,095,803 bp (29.48%) number of G's = 37,082,578 bp (20.98%) number of N's = 2,665 bp (0%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,079,054 number of insertions = 26,417 mapped reads with insertion percentage = 1.33% number of deletions = 57,851 mapped reads with deletion percentage = 2.96% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.7204X There is a 3.9% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 16316187 0.0654609682998543 1.136433709901318 chr2 243199373 11262646 0.046310341433322695 1.0496406718948827 chr3 198022430 11296982 0.0570490019741703 0.3213584676875496 chr4 191154276 8549857 0.04472752155437004 0.37697647538473533 chr5 180915260 10356626 0.05724572929889939 0.34280430245455307 chr6 171115067 7766658 0.045388510410950544 0.32518087217105646 chr7 159138663 15319796 0.09626696436427896 1.5791188211589446 chr8 146364022 18601579 0.12709119868269267 0.6329247834571402 chr9 141213431 6231209 0.04412617805455063 0.5272468171716417 chr10 135534747 7870574 0.05807052563428624 0.8697967097914482 chr11 135006516 7498873 0.05554452645826369 0.39063564662307637 chr12 133851895 6578071 0.049144399487209355 0.30128612702133367 chr13 115169878 5873544 0.050998959988478934 0.3066515809273736 chr14 107349540 5276599 0.049153438384551995 0.328658163531006 chr15 102531392 4730516 0.046137245459419884 0.2885720884830482 chr16 90354753 4127662 0.04568284304866618 0.7278096549803131 chr17 81195210 4340782 0.05346106007977564 0.41416765203598815 chr18 78077248 3036650 0.038892892331451025 0.5872054346700666 chr19 59128983 2905703 0.049141771980079546 1.03197614857372 chr20 63025520 6988545 0.11088436874459742 0.48711897136654225 chr21 48129895 2060716 0.042815717757123714 0.3181327691420438 chr22 51304566 1549006 0.03019236143621213 0.2767533416573965 chrMT 16571 656186 39.59845513246032 22.88475243031471 chrX 155270560 7035027 0.04530818334138809 0.353802440999041 chrY 59373566 600475 0.010113507415067507 0.7967370402349379