BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124964.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,232,644 number of mapped reads = 3,937,556 (93.03%) number of supplementary alignments = 13,924 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,006,021 number of mapped paired reads (second in pair) = 1,931,535 number of mapped paired reads (both in pair) = 3,833,984 number of mapped paired reads (singletons) = 103,572 number of mapped bases = 240,578,094 bp number of sequenced bases = 240,447,569 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 380,533 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 75,739.3403 std insert size = 2,599,067.6316 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 51.4455 >>>>>>> ACTG content number of A's = 66,876,417 bp (27.81%) number of C's = 42,677,063 bp (17.75%) number of T's = 72,890,328 bp (30.31%) number of G's = 58,003,761 bp (24.12%) number of N's = 0 bp (0%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,005,923 number of insertions = 33,669 mapped reads with insertion percentage = 0.84% number of deletions = 79,353 mapped reads with deletion percentage = 1.99% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.0777X std coverageData = 1.1522X There is a 5.75% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.09% 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 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 19493153 0.0782070388502663 0.5929455038112452 chr2 243199373 21267070 0.08744705933102878 1.211375589298614 chr3 198022430 16010670 0.08085281046192595 0.4207148817588817 chr4 191154276 14713736 0.07697309371201301 1.020467380205334 chr5 180915260 13817642 0.07637632115720919 0.35533842430476686 chr6 171115067 13508786 0.07894562551876276 0.44861940401371914 chr7 159138663 14868903 0.09343363026746053 0.6491122180702732 chr8 146364022 14266954 0.0974758264022015 0.45068527318097085 chr9 141213431 9570858 0.06777583358908686 0.6821805598007844 chr10 135534747 14081399 0.1038951214480815 4.022472951482712 chr11 135006516 9376511 0.06945228480675703 0.42136737149276393 chr12 133851895 10652263 0.07958245940410481 0.35198556944417747 chr13 115169878 6061048 0.052627024576686623 0.27802178991548765 chr14 107349540 7877601 0.07338271780205113 0.3858526128091536 chr15 102531392 6461310 0.06301787066345496 0.3196700139598122 chr16 90354753 9540585 0.10559029473524209 2.166069315877953 chr17 81195210 5326275 0.06559838936311638 0.5664579150801377 chr18 78077248 4918264 0.0629922816951745 0.8930665977843584 chr19 59128983 3753032 0.06347195249409245 0.5105032931920661 chr20 63025520 5148163 0.08168378460026986 0.518386634681617 chr21 48129895 2771436 0.057582423564397966 0.5834113803613779 chr22 51304566 2229932 0.04346459143616964 0.30321215651539807 chrMT 16571 96696 5.8352543600265525 4.360246254084804 chrX 155270560 8881360 0.05719925271088093 0.37954251526735033 chrY 59373566 5884447 0.099108869425158 2.438240218603984