BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927020.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 = 35,027,056 number of mapped reads = 34,530,215 (98.58%) number of supplementary alignments = 329,327 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,306,190 number of mapped paired reads (second in pair) = 17,224,025 number of mapped paired reads (both in pair) = 34,240,960 number of mapped paired reads (singletons) = 289,255 number of mapped bases = 3,264,726,081 bp number of sequenced bases = 3,262,310,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,613,664 duplication rate = 5.77% >>>>>>> Insert size mean insert size = 92,427.9958 std insert size = 2,979,431.648 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.473 >>>>>>> ACTG content number of A's = 939,837,076 bp (28.81%) number of C's = 648,434,228 bp (19.88%) number of T's = 949,247,588 bp (29.1%) number of G's = 724,088,580 bp (22.2%) number of N's = 702,672 bp (0.02%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 29,858,075 number of insertions = 520,488 mapped reads with insertion percentage = 1.48% number of deletions = 1,707,111 mapped reads with deletion percentage = 4.82% homopolymer indels = 53.09% >>>>>>> Coverage mean coverageData = 1.0546X std coverageData = 4.6952X There is a 37.65% of reference with a coverageData >= 1X There is a 22.57% of reference with a coverageData >= 2X There is a 13.98% of reference with a coverageData >= 3X There is a 9.08% of reference with a coverageData >= 4X There is a 6.05% of reference with a coverageData >= 5X There is a 4.12% of reference with a coverageData >= 6X There is a 2.85% of reference with a coverageData >= 7X There is a 2% of reference with a coverageData >= 8X There is a 1.42% of reference with a coverageData >= 9X There is a 1.02% of reference with a coverageData >= 10X There is a 0.73% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 267075805 1.071515103667485 6.930351961118715 chr2 243199373 286477017 1.1779512975964785 6.792359909910495 chr3 198022430 220975582 1.1159118792754943 2.1576787824438415 chr4 191154276 200194281 1.047291670315552 3.1840181115818598 chr5 180915260 200188335 1.1065309526681166 2.0763329062245703 chr6 171115067 187639516 1.0965692226272512 2.1646103126860274 chr7 159138663 167118761 1.0501455639350195 3.147298975315764 chr8 146364022 166822548 1.1397783807826762 2.5502219961729975 chr9 141213431 137856228 0.9762260361764031 4.967262455153141 chr10 135534747 162574587 1.199504854648085 11.699072121514723 chr11 135006516 155877826 1.1545948345189503 5.3374864954975205 chr12 133851895 146360566 1.093451579449062 2.0998150070921366 chr13 115169878 100217794 0.8701736577336654 1.8366652146268276 chr14 107349540 99192669 0.9240157805985941 1.9805511816174715 chr15 102531392 93801008 0.9148515997910182 1.9572003879137656 chr16 90354753 103418979 1.144588143581113 6.711605672254083 chr17 81195210 82608758 1.0174092535754264 2.579536114071237 chr18 78077248 88636761 1.1352444312586427 5.210347193720305 chr19 59128983 49617489 0.8391399020003439 3.834380497204249 chr20 63025520 75471399 1.1974736424229424 2.443617361112822 chr21 48129895 42577065 0.8846282544352112 3.065792438179718 chr22 51304566 39004185 0.7602478305732087 1.8916051974964938 chrMT 16571 208125 12.559592058415303 10.680565182515396 chrX 155270560 185203576 1.1927797259184227 2.8362074541710167 chrY 59373566 5607221 0.09443968718335025 2.7767477442464763