BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927024.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 9,207,806 number of mapped reads = 8,980,839 (97.54%) number of supplementary alignments = 294,003 (3.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,509,481 number of mapped paired reads (second in pair) = 4,471,358 number of mapped paired reads (both in pair) = 8,842,506 number of mapped paired reads (singletons) = 138,333 number of mapped bases = 820,829,160 bp number of sequenced bases = 820,195,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 500,634 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 350,480.6792 std insert size = 5,811,399.0811 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 52.3474 >>>>>>> ACTG content number of A's = 235,439,545 bp (28.71%) number of C's = 159,191,742 bp (19.41%) number of T's = 240,013,416 bp (29.26%) number of G's = 185,398,067 bp (22.6%) number of N's = 153,017 bp (0.02%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 8,075,274 number of insertions = 144,831 mapped reads with insertion percentage = 1.58% number of deletions = 429,254 mapped reads with deletion percentage = 4.66% homopolymer indels = 51.75% >>>>>>> Coverage mean coverageData = 0.2652X std coverageData = 1.3523X There is a 16.84% of reference with a coverageData >= 1X There is a 5.84% of reference with a coverageData >= 2X There is a 1.97% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 67428819 0.2705261825606445 1.4666848522423492 chr2 243199373 72860218 0.2995904845527706 1.9860381486379624 chr3 198022430 55921190 0.2823982616514705 0.7500428268877012 chr4 191154276 50573857 0.26457089037338616 0.939056611809827 chr5 180915260 50899195 0.28134274024203376 0.7248288323220062 chr6 171115067 47656951 0.27850820991701447 0.8038500996540946 chr7 159138663 42177333 0.26503510966407956 0.974951103050221 chr8 146364022 42289684 0.2889349679117181 0.8338090961866417 chr9 141213431 34408928 0.24366611416728484 1.653450826384128 chr10 135534747 41206628 0.3040299916596295 3.3327230936280605 chr11 135006516 38821905 0.2875557873073326 1.5787620766779256 chr12 133851895 36512149 0.27278021726924373 0.720649216099437 chr13 115169878 25160165 0.21846133239804247 0.6340732267179696 chr14 107349540 24469733 0.22794446068422836 0.6747973090385139 chr15 102531392 23162465 0.22590608152476854 0.657933846234895 chr16 90354753 26062858 0.28845032645930646 2.0673060405988117 chr17 81195210 20037653 0.24678368342171908 0.7697956130287603 chr18 78077248 22030684 0.2821652218069981 1.7515482247799266 chr19 59128983 12468659 0.21087220458366415 0.9933794822200834 chr20 63025520 18321694 0.2907027819841867 0.7777087457847065 chr21 48129895 10356218 0.21517225416760208 0.8091056480986264 chr22 51304566 9471940 0.1846217742101161 0.6217448806652408 chrMT 16571 27211 1.642085571178565 2.0246107437339336 chrX 155270560 46991393 0.3026420011623581 0.889805437289663 chrY 59373566 1511630 0.025459646469609052 0.8124759431417664