BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006410.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 = 6,563,710 number of mapped reads = 5,734,879 (87.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,896,684 number of mapped paired reads (second in pair) = 2,838,195 number of mapped paired reads (both in pair) = 5,204,032 number of mapped paired reads (singletons) = 530,847 number of mapped bases = 221,976,034 bp number of sequenced bases = 221,945,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,714 duplication rate = 3% >>>>>>> Insert size mean insert size = 82,793.3643 std insert size = 2,733,474.742 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 48.1189 >>>>>>> ACTG content number of A's = 62,494,355 bp (28.16%) number of C's = 46,951,201 bp (21.15%) number of T's = 63,711,536 bp (28.71%) number of G's = 48,779,047 bp (21.98%) number of N's = 9,148 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 765,512 number of insertions = 6,112 mapped reads with insertion percentage = 0.11% number of deletions = 22,628 mapped reads with deletion percentage = 0.39% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 0.0717X std coverageData = 0.4312X There is a 6.01% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 18120990 0.07270188506370863 0.5701797430245638 chr2 243199373 18225344 0.07493993004661241 0.38667663552738213 chr3 198022430 14712877 0.07429904279025361 0.3124360416390999 chr4 191154276 14070270 0.07360688075845083 0.32831185588231865 chr5 180915260 13707748 0.07576888759964195 0.3157536832844818 chr6 171115067 13057523 0.07630843518881947 0.34935111348874687 chr7 159138663 12134256 0.07624957864576254 0.4817934522294729 chr8 146364022 11357390 0.0775968700832777 1.005021464671502 chr9 141213431 9094251 0.06440075094556692 0.3419515898065912 chr10 135534747 10635242 0.07846874868184171 0.39595772880099084 chr11 135006516 10305537 0.07633362674139373 0.3847521559836757 chr12 133851895 10095485 0.0754228021949185 0.3176607951920307 chr13 115169878 7075148 0.06143227832541422 0.28222248961019497 chr14 107349540 6854114 0.06384856423231995 0.3211206155898148 chr15 102531392 6416868 0.06258442292483457 0.2872193920174865 chr16 90354753 6603449 0.07308358200038464 0.35224021729400173 chr17 81195210 5990248 0.07377587914360959 0.33499999851899437 chr18 78077248 5928831 0.0759354504912878 0.5704643428447018 chr19 59128983 4265807 0.0721440955613933 0.4464769030359947 chr20 63025520 4861267 0.07713172378427025 0.32735491476329565 chr21 48129895 2881443 0.05986805082371362 0.3079553935354579 chr22 51304566 2743111 0.05346719042511733 0.27332238873193077 chrMT 16571 6228 0.3758373061372277 0.7731417658188878 chrX 155270560 12344794 0.07950505234218258 0.3550078051428712 chrY 59373566 487813 0.008215996324020694 0.1851601599173906