BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975314.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,587,888 number of mapped reads = 2,561,296 (98.97%) number of supplementary alignments = 27,619 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,283,082 number of mapped paired reads (second in pair) = 1,278,214 number of mapped paired reads (both in pair) = 2,552,944 number of mapped paired reads (singletons) = 8,352 number of mapped bases = 345,502,288 bp number of sequenced bases = 345,268,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 381,091 duplication rate = 14.82% >>>>>>> Insert size mean insert size = 75,248.7705 std insert size = 2,620,284.3999 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.7817 >>>>>>> ACTG content number of A's = 99,719,149 bp (28.88%) number of C's = 70,765,724 bp (20.5%) number of T's = 100,397,319 bp (29.08%) number of G's = 74,363,536 bp (21.54%) number of N's = 22,926 bp (0.01%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 3,405,163 number of insertions = 60,513 mapped reads with insertion percentage = 2.25% number of deletions = 123,245 mapped reads with deletion percentage = 4.65% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.1116X std coverageData = 1.1475X There is a 6.38% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 29017970 0.11642085337071237 1.153838722810904 chr2 243199373 29177713 0.11997445815783415 1.1771681755971266 chr3 198022430 23992029 0.1211581384997649 0.49951968655965506 chr4 191154276 21873433 0.11442816481908048 0.767414536237938 chr5 180915260 21071948 0.11647413269615842 0.47201870733255114 chr6 171115067 27034244 0.1579886825512566 0.9795858348285682 chr7 159138663 19937208 0.1252819875708017 1.286876333761191 chr8 146364022 17061947 0.11657200155376982 0.5668743435498275 chr9 141213431 15188159 0.10755463479957512 1.8990645728468467 chr10 135534747 18417428 0.13588713158552618 2.902519815638768 chr11 135006516 12496959 0.09256559883376296 1.1718857023252947 chr12 133851895 15103758 0.11283932887166073 0.4623176561875792 chr13 115169878 11456556 0.09947528120156557 0.43821473308663156 chr14 107349540 10299436 0.09594299146507754 0.4401920367976853 chr15 102531392 10089116 0.09840026359926919 0.43380446307679543 chr16 90354753 11511455 0.12740287165634773 1.6111163298310818 chr17 81195210 7432242 0.09153547358273967 1.0612287940762541 chr18 78077248 9313136 0.1192810484303955 1.7244058266165192 chr19 59128983 4712086 0.0796916463115897 0.7644744895524662 chr20 63025520 7546974 0.11974473197523797 0.5188838460271933 chr21 48129895 4417854 0.09179022725896244 0.5751930649026568 chr22 51304566 3695385 0.0720283843742095 0.3739962428722833 chrMT 16571 53922 3.253997948222799 2.7449679835602327 chrX 155270560 10520814 0.06775794458395719 0.48893498153986414 chrY 59373566 4080516 0.06872613984479221 1.4903368726195654