BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080553.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 = 2,660,247 number of mapped reads = 2,194,389 (82.49%) number of supplementary alignments = 13,196 (0.5%) number of secondary alignments = 0 number of mapped bases = 145,014,940 bp number of sequenced bases = 144,952,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,483 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4343 >>>>>>> ACTG content number of A's = 39,603,982 bp (27.32%) number of C's = 25,562,983 bp (17.64%) number of T's = 47,601,711 bp (32.84%) number of G's = 32,067,776 bp (22.12%) number of N's = 115,721 bp (0.08%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,334,924 number of insertions = 12,387 mapped reads with insertion percentage = 0.56% number of deletions = 38,050 mapped reads with deletion percentage = 1.71% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.0468X std coverageData = 0.3726X There is a 3.88% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 11548273 0.046331972829869096 0.5874905556302377 chr2 243199373 12324551 0.0506767383812293 0.36890099948450067 chr3 198022430 9865670 0.049820972300966104 0.2606124444909968 chr4 191154276 9772386 0.05112303111649985 0.2812616786054321 chr5 180915260 8982153 0.049648398924446724 0.2595045705850467 chr6 171115067 8598504 0.05024983568512994 0.3135633942768827 chr7 159138663 8108748 0.05095397841817988 0.5957990927747836 chr8 146364022 7690567 0.05254410814154861 0.5760678372818762 chr9 141213431 5970129 0.04227734541766073 0.33220274345250905 chr10 135534747 6805766 0.05021417865634117 0.37042454573893413 chr11 135006516 6451133 0.04778386400253452 0.30483221636115776 chr12 133851895 6499272 0.048555696577922934 0.26023790734054575 chr13 115169878 4828017 0.041920831070082404 0.23855940851549362 chr14 107349540 4403935 0.041024255902726736 0.2506678682523584 chr15 102531392 3994991 0.038963588829458204 0.22919495220261027 chr16 90354753 3814411 0.042215941866389696 0.26590311291475466 chr17 81195210 3588975 0.04420180697851511 0.2651192783155024 chr18 78077248 3887761 0.049793776030630586 0.5379596398590135 chr19 59128983 2526744 0.04273274918325587 0.4213497579008929 chr20 63025520 2878649 0.04567433953738105 0.2572027914802566 chr21 48129895 1973062 0.04099452118065082 0.2580439984009978 chr22 51304566 1502542 0.029286711050240635 0.1980430967732316 chrMT 16571 132318 7.984913402932834 12.269006793834565 chrX 155270560 8489900 0.0546781051089144 0.2972832079271478 chrY 59373566 376483 0.006340919459006387 0.16480578882930594