BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080613.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,372,430 number of mapped reads = 2,857,752 (84.74%) number of supplementary alignments = 22,490 (0.67%) number of secondary alignments = 0 number of mapped bases = 191,114,605 bp number of sequenced bases = 191,038,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,232 duplication rate = 4.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5851 >>>>>>> ACTG content number of A's = 52,884,593 bp (27.68%) number of C's = 34,237,093 bp (17.92%) number of T's = 61,792,803 bp (32.35%) number of G's = 41,963,462 bp (21.97%) number of N's = 160,187 bp (0.08%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,723,291 number of insertions = 15,554 mapped reads with insertion percentage = 0.54% number of deletions = 46,212 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0617X std coverageData = 0.4055X There is a 4.89% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 15111894 0.06062931333679606 0.5378755967022301 chr2 243199373 16036902 0.06594137888669639 0.4450280591279327 chr3 198022430 13208628 0.06670268615530069 0.3155544059850853 chr4 191154276 12418673 0.06496675491580424 0.32254772894090433 chr5 180915260 12238726 0.06764894238330144 0.3161156827742558 chr6 171115067 11440840 0.06686050621129698 0.3746390746444771 chr7 159138663 10223009 0.06423963106941523 0.6461474408733419 chr8 146364022 8883388 0.060693795364546624 0.5110266670323079 chr9 141213431 7987558 0.0565637272845527 0.3794539263819879 chr10 135534747 8969995 0.06618225361795968 0.40925018478958963 chr11 135006516 8667167 0.06419813840688993 0.3729033888107806 chr12 133851895 9135562 0.0682512713025094 0.32042817397727613 chr13 115169878 6429029 0.05582213953547819 0.2875897743827048 chr14 107349540 5916212 0.05511166605837342 0.3033367911636932 chr15 102531392 5360127 0.052277911139643946 0.2768144641328898 chr16 90354753 5039713 0.05577695508724372 0.3180213316417212 chr17 81195210 4818870 0.059349190672701016 0.3289256564899325 chr18 78077248 5217719 0.06682764997044978 0.6636946139414484 chr19 59128983 3236371 0.05473408869555561 0.45728093836029476 chr20 63025520 4072706 0.06461995077549539 0.31672544083878024 chr21 48129895 2756264 0.05726719329015781 0.3105144579144807 chr22 51304566 1986612 0.03872193363842119 0.23774309775395064 chrMT 16571 26212 1.5817995292981715 2.5071178995622554 chrX 155270560 11472238 0.07388546805009269 0.3521710542325747 chrY 59373566 460190 0.007750755614038746 0.15318408468148198