BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971300.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,550,443 number of mapped reads = 8,989,661 (85.21%) number of secondary alignments = 0 number of mapped bases = 354,160,926 bp number of sequenced bases = 354,126,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 742,270 duplication rate = 6.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.2706 >>>>>>> ACTG content number of A's = 100,598,595 bp (28.41%) number of C's = 73,722,016 bp (20.82%) number of T's = 103,902,879 bp (29.34%) number of G's = 75,899,811 bp (21.43%) number of N's = 2,717 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,163,998 number of insertions = 13,034 mapped reads with insertion percentage = 0.14% number of deletions = 28,040 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.18% >>>>>>> Coverage mean coverageData = 0.1144X std coverageData = 1.1106X There is a 8.81% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.11% 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 0.01% 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% 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 32052770 0.12859655021681973 2.539455139065664 chr2 243199373 30181400 0.12410147126489508 0.9160270321881617 chr3 198022430 24208626 0.12225193883339378 0.4392861071270652 chr4 191154276 23417507 0.12250579735919692 0.4940887126286738 chr5 180915260 22254210 0.12300902643591259 0.47711150387929285 chr6 171115067 20958645 0.12248275600418052 0.5810165004870951 chr7 159138663 19969434 0.12548449021467523 1.419282021266903 chr8 146364022 18306827 0.1250773704483196 1.6444305879389947 chr9 141213431 14855843 0.10520134589747344 0.9157057853071089 chr10 135534747 16639777 0.12277129937756846 0.9923457862603713 chr11 135006516 16197202 0.11997348335394419 0.7576301849913523 chr12 133851895 16151617 0.12066782468787611 0.48278778473802003 chr13 115169878 11335386 0.09842318318683987 0.37711269081537563 chr14 107349540 10890121 0.10144543702748983 0.5284654784488176 chr15 102531392 9733276 0.09492971674470195 0.37993622157188733 chr16 90354753 9486115 0.10498744875103581 0.5083148773540884 chr17 81195210 8870785 0.10925256551464058 0.4623986502800757 chr18 78077248 9390644 0.1202737575996531 1.7931262472445724 chr19 59128983 7233235 0.1223297718480969 2.2258424317210466 chr20 63025520 6891703 0.10934781656700333 0.46975369973901315 chr21 48129895 4402739 0.09147618127984697 0.5078915822504155 chr22 51304566 3631265 0.07077859307883044 0.40334316177257545 chrMT 16571 57642 3.4784865125822217 3.6516987746193577 chrX 155270560 13672614 0.08805670566268325 0.5603366286189313 chrY 59373566 3371543 0.05678525355879753 0.5137085589054099