BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777263.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 61,526,560 number of mapped reads = 61,334,618 (99.69%) number of supplementary alignments = 1,994,815 (3.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,670,384 number of mapped paired reads (second in pair) = 30,664,234 number of mapped paired reads (both in pair) = 61,255,314 number of mapped paired reads (singletons) = 79,304 number of mapped bases = 6,150,640,746 bp number of sequenced bases = 6,149,759,733 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,053,361 duplication rate = 40.73% >>>>>>> Insert size mean insert size = 314,370.574 std insert size = 5,474,873.3244 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.6707 >>>>>>> ACTG content number of A's = 1,684,254,948 bp (27.39%) number of C's = 1,376,580,585 bp (22.38%) number of T's = 1,671,470,259 bp (27.18%) number of G's = 1,388,503,204 bp (22.58%) number of N's = 28,950,737 bp (0.47%) GC percentage = 44.96% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 43,186,467 number of insertions = 953,489 mapped reads with insertion percentage = 1.53% number of deletions = 418,047 mapped reads with deletion percentage = 0.67% homopolymer indels = 50.16% >>>>>>> Coverage mean coverageData = 1.9868X std coverageData = 16.7195X There is a 21.26% of reference with a coverageData >= 1X There is a 11.17% of reference with a coverageData >= 2X There is a 6.84% of reference with a coverageData >= 3X There is a 5.06% of reference with a coverageData >= 4X There is a 4.1% of reference with a coverageData >= 5X There is a 3.58% of reference with a coverageData >= 6X There is a 3.23% of reference with a coverageData >= 7X There is a 2.99% of reference with a coverageData >= 8X There is a 2.8% of reference with a coverageData >= 9X There is a 2.65% of reference with a coverageData >= 10X There is a 2.52% of reference with a coverageData >= 11X There is a 2.41% of reference with a coverageData >= 12X There is a 2.31% of reference with a coverageData >= 13X There is a 2.22% of reference with a coverageData >= 14X There is a 2.14% of reference with a coverageData >= 15X There is a 2.07% of reference with a coverageData >= 16X There is a 2% of reference with a coverageData >= 17X There is a 1.94% of reference with a coverageData >= 18X There is a 1.88% of reference with a coverageData >= 19X There is a 1.83% of reference with a coverageData >= 20X There is a 1.77% of reference with a coverageData >= 21X There is a 1.72% of reference with a coverageData >= 22X There is a 1.68% of reference with a coverageData >= 23X There is a 1.63% of reference with a coverageData >= 24X There is a 1.59% of reference with a coverageData >= 25X There is a 1.55% of reference with a coverageData >= 26X There is a 1.51% of reference with a coverageData >= 27X There is a 1.48% of reference with a coverageData >= 28X There is a 1.44% of reference with a coverageData >= 29X There is a 1.41% of reference with a coverageData >= 30X There is a 1.38% of reference with a coverageData >= 31X There is a 1.34% of reference with a coverageData >= 32X There is a 1.31% of reference with a coverageData >= 33X There is a 1.29% of reference with a coverageData >= 34X There is a 1.26% of reference with a coverageData >= 35X There is a 1.23% of reference with a coverageData >= 36X There is a 1.21% of reference with a coverageData >= 37X There is a 1.18% of reference with a coverageData >= 38X There is a 1.16% of reference with a coverageData >= 39X There is a 1.13% of reference with a coverageData >= 40X There is a 1.11% of reference with a coverageData >= 41X There is a 1.09% of reference with a coverageData >= 42X There is a 1.07% of reference with a coverageData >= 43X There is a 1.05% of reference with a coverageData >= 44X There is a 1.03% of reference with a coverageData >= 45X There is a 1.01% of reference with a coverageData >= 46X There is a 0.99% of reference with a coverageData >= 47X There is a 0.97% of reference with a coverageData >= 48X There is a 0.95% of reference with a coverageData >= 49X There is a 0.94% of reference with a coverageData >= 50X There is a 0.92% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 521047394 2.0904557505595944 15.658909939008742 chr2 243199373 561931080 2.310577831958473 18.281806754512914 chr3 198022430 385355908 1.9460215087755464 16.77674472946659 chr4 191154276 282431314 1.4775045576275783 14.112513993040514 chr5 180915260 262191462 1.4492501185361588 13.144716643031515 chr6 171115067 297771643 1.7401836566501767 14.647329796230396 chr7 159138663 398515985 2.504205938942694 19.89162498124802 chr8 146364022 207407027 1.417062910446667 14.063142175208535 chr9 141213431 220225348 1.559521261118569 14.056920956563712 chr10 135534747 265955455 1.962267690660905 15.844076211022507 chr11 135006516 441341364 3.2690375033453942 24.19348677487569 chr12 133851895 352491367 2.6334432321634296 18.828604302744512 chr13 115169878 185779613 1.6130920360964522 16.030998639220293 chr14 107349540 137877219 1.2843764304905265 11.342811914579814 chr15 102531392 307360357 2.9977195374466388 23.244394216476145 chr16 90354753 189286619 2.0949270814784917 15.55107253233596 chr17 81195210 280690542 3.4569840018887814 22.99851871464851 chr18 78077248 98219452 1.2579778938929815 11.901408040701849 chr19 59128983 297154571 5.025531573915282 28.996652691928386 chr20 63025520 173154007 2.7473634013650345 20.486211676099295 chr21 48129895 40569671 0.8429204136015672 8.974445322254981 chr22 51304566 70054512 1.365463495003544 10.991524465157509 chrMT 16571 1527585 92.18423752338423 32.60244976355925 chrX 155270560 170601662 1.0987379835559297 10.715038250842538 chrY 59373566 1699589 0.02862534818946196 0.986764955471093