BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779167.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 34,209,704 number of mapped reads = 33,413,851 (97.67%) number of supplementary alignments = 203,955 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,783,082 number of mapped paired reads (second in pair) = 16,630,769 number of mapped paired reads (both in pair) = 33,147,766 number of mapped paired reads (singletons) = 266,085 number of mapped bases = 3,336,525,385 bp number of sequenced bases = 3,335,777,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,136,894 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 79,531.8618 std insert size = 2,663,841.4878 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.533 >>>>>>> ACTG content number of A's = 1,020,889,155 bp (30.6%) number of C's = 645,629,877 bp (19.35%) number of T's = 1,011,339,805 bp (30.32%) number of G's = 656,558,046 bp (19.68%) number of N's = 1,360,564 bp (0.04%) GC percentage = 39.04% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 13,491,652 number of insertions = 273,011 mapped reads with insertion percentage = 0.81% number of deletions = 335,088 mapped reads with deletion percentage = 0.98% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 1.0778X std coverageData = 2.3907X There is a 40.37% of reference with a coverageData >= 1X There is a 23.73% of reference with a coverageData >= 2X There is a 14.21% of reference with a coverageData >= 3X There is a 8.96% of reference with a coverageData >= 4X There is a 5.83% of reference with a coverageData >= 5X There is a 3.91% of reference with a coverageData >= 6X There is a 2.68% of reference with a coverageData >= 7X There is a 1.88% of reference with a coverageData >= 8X There is a 1.35% of reference with a coverageData >= 9X There is a 0.98% of reference with a coverageData >= 10X There is a 0.73% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 237300987 0.952057756357606 2.785440492123195 chr2 243199373 196226901 0.8068561138930239 2.0811159008516684 chr3 198022430 236604983 1.1948393068401393 2.069721220703798 chr4 191154276 231746283 1.2123520741958187 2.08963140414326 chr5 180915260 265986399 1.4702264419264577 2.3005842626698683 chr6 171115067 163676587 0.9565293686265511 1.885283011962707 chr7 159138663 279034461 1.7534045827694305 4.050839574148344 chr8 146364022 236240630 1.6140621634461507 2.6100988826559774 chr9 141213431 132606246 0.9390483968908029 2.0027873827699283 chr10 135534747 80284605 0.5923544093087805 3.2603403166866816 chr11 135006516 168948115 1.251407117268325 2.1723096636857866 chr12 133851895 150087256 1.121293471414805 2.07601624089002 chr13 115169878 138678542 1.2041216367356056 2.1832194721337888 chr14 107349540 121267461 1.1296504950091075 2.1296643836200984 chr15 102531392 85965883 0.8384347595710004 1.8718155251026296 chr16 90354753 71129554 0.7872253715308147 1.7053436875155787 chr17 81195210 57337959 0.7061741573179009 1.7393083701023646 chr18 78077248 61643064 0.7895137902401478 1.637638500436678 chr19 59128983 32696723 0.552972862732985 1.9212001527531088 chr20 63025520 67973446 1.0785067064896887 2.106938199970952 chr21 48129895 28887264 0.6001937880811915 1.5248179658691676 chr22 51304566 17723186 0.3454504614657495 1.0673456047892187 chrMT 16571 1671 0.1008388147969344 0.4047346918771635 chrX 155270560 272341004 1.753977083614563 2.9989784596063744 chrY 59373566 2136175 0.03597855314939311 0.485506387083827