BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006190.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 = 8,474,868 number of mapped reads = 4,619,099 (54.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,326,876 number of mapped paired reads (second in pair) = 2,292,223 number of mapped paired reads (both in pair) = 4,240,986 number of mapped paired reads (singletons) = 378,113 number of mapped bases = 178,805,342 bp number of sequenced bases = 178,780,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,873 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 55,363.4633 std insert size = 2,256,560.7879 median insert size = 114 >>>>>>> Mapping quality mean mapping quality = 47.8471 >>>>>>> ACTG content number of A's = 49,099,801 bp (27.46%) number of C's = 39,137,667 bp (21.89%) number of T's = 50,065,002 bp (28%) number of G's = 40,456,837 bp (22.63%) number of N's = 20,949 bp (0.01%) GC percentage = 44.52% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 558,502 number of insertions = 5,366 mapped reads with insertion percentage = 0.12% number of deletions = 18,590 mapped reads with deletion percentage = 0.4% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.3854X There is a 4.67% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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% 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 15184815 0.06092187429294309 0.4445314102900879 chr2 243199373 15412090 0.06337224397367176 0.40438824077750885 chr3 198022430 12291427 0.06207088257628189 0.295607358512226 chr4 191154276 11168831 0.058428360765521145 0.28904022264404017 chr5 180915260 11044443 0.06104760317067781 0.39920693670468943 chr6 171115067 10227954 0.05977237527540459 0.3270379999382356 chr7 159138663 9497098 0.05967813114026225 0.4050274987455214 chr8 146364022 9134848 0.0624118405273121 0.7271115865209496 chr9 141213431 7322978 0.05185751771727719 0.30437124840842655 chr10 135534747 8303889 0.0612676024694981 0.3299180412400425 chr11 135006516 8272185 0.061272487025737336 0.342507718430985 chr12 133851895 8071109 0.060298802643025715 0.2949133890447154 chr13 115169878 5191851 0.04507993834985221 0.25342491139166945 chr14 107349540 5654832 0.05267681631425714 0.6673360471378246 chr15 102531392 5319456 0.051881242380870045 0.2719408905398937 chr16 90354753 5563829 0.061577601789249536 0.3215545339193639 chr17 81195210 5062975 0.062355587232301016 0.3181894005757141 chr18 78077248 4540204 0.05815015406280713 0.4303447393297245 chr19 59128983 3692892 0.062454853992668875 0.3759677978016456 chr20 63025520 3882029 0.061594557252363805 0.3022783279994978 chr21 48129895 2297864 0.04774296723481321 0.2785777207851955 chr22 51304566 2343501 0.04567821507348878 0.2754691293593484 chrMT 16571 1318 0.07953653973809667 0.4106430541518495 chrX 155270560 8977976 0.0578214955880883 0.29860985864037 chrY 59373566 344948 0.005809790841937976 0.12710217613543529