BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006396.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 6,423,000 number of mapped reads = 5,046,401 (78.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,556,704 number of mapped paired reads (second in pair) = 2,489,697 number of mapped paired reads (both in pair) = 4,642,242 number of mapped paired reads (singletons) = 404,159 number of mapped bases = 195,481,772 bp number of sequenced bases = 195,458,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,763 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 67,261.6911 std insert size = 2,467,249.3315 median insert size = 145 >>>>>>> Mapping quality mean mapping quality = 48.4987 >>>>>>> ACTG content number of A's = 55,300,387 bp (28.29%) number of C's = 41,646,845 bp (21.31%) number of T's = 55,693,850 bp (28.49%) number of G's = 42,808,830 bp (21.9%) number of N's = 8,403 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 711,258 number of insertions = 5,230 mapped reads with insertion percentage = 0.1% number of deletions = 17,498 mapped reads with deletion percentage = 0.35% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 0.0631X std coverageData = 0.3905X There is a 5.42% of reference with a coverageData >= 1X There is a 0.69% 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 16494044 0.0661745352281389 0.5088443015125327 chr2 243199373 16829499 0.06920042100601961 0.37413584610939404 chr3 198022430 13420674 0.06777350424393842 0.29119989347103836 chr4 191154276 12200532 0.06382557720027147 0.3180300414145586 chr5 180915260 11698089 0.06466059855868432 0.314442545306639 chr6 171115067 11162496 0.06523385810321425 0.31479086923111355 chr7 159138663 10472792 0.06580922450001983 0.42073950002958593 chr8 146364022 9740163 0.06654752217727386 0.8779744827031324 chr9 141213431 8183851 0.05795377211676133 0.3034339752388026 chr10 135534747 9270018 0.06839587784820965 0.4132567616787174 chr11 135006516 8719829 0.06458820846839719 0.33282491732494296 chr12 133851895 8897201 0.06647048964080784 0.2900813243221441 chr13 115169878 6040710 0.05245043326346147 0.25552158345234 chr14 107349540 5910993 0.055063049175618266 0.2764386059941483 chr15 102531392 5617313 0.05478627462699424 0.26236533033513787 chr16 90354753 6016064 0.06658270650133923 0.353025242681143 chr17 81195210 5152592 0.06345930997653679 0.2944307087351886 chr18 78077248 4900062 0.06275915360131545 0.4585264591555697 chr19 59128983 3817216 0.06455744385118209 0.39779910527657425 chr20 63025520 4489871 0.0712389362277376 0.311951962887642 chr21 48129895 2503454 0.05201453275557738 0.29345791537624455 chr22 51304566 2403483 0.04684735077965575 0.24603394896811134 chrMT 16571 1661 0.10023535091424778 0.3336307258562633 chrX 155270560 11019690 0.07097089106911188 0.3165739713313118 chrY 59373566 519475 0.008749263940117729 0.2280885184193159