BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472546.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,856,508 number of mapped reads = 15,680,236 (98.89%) number of supplementary alignments = 68,263 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,857,548 number of mapped paired reads (second in pair) = 7,822,688 number of mapped paired reads (both in pair) = 15,594,662 number of mapped paired reads (singletons) = 85,574 number of mapped bases = 1,537,649,306 bp number of sequenced bases = 1,537,453,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,615,482 duplication rate = 45.05% >>>>>>> Insert size mean insert size = 30,679.2358 std insert size = 1,713,443.7104 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 55.0094 >>>>>>> ACTG content number of A's = 421,362,842 bp (27.41%) number of C's = 349,846,265 bp (22.75%) number of T's = 418,738,794 bp (27.24%) number of G's = 347,269,431 bp (22.59%) number of N's = 236,161 bp (0.02%) GC percentage = 45.34% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,858,127 number of insertions = 80,535 mapped reads with insertion percentage = 0.51% number of deletions = 75,792 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.4967X std coverageData = 16.9113X There is a 5.16% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174064780 0.6983524426203938 20.45054643668858 chr2 243199373 114713528 0.47168513053691136 17.46800742353194 chr3 198022430 146756863 0.7411123224778122 16.369825986089637 chr4 191154276 56764692 0.29695747951774826 12.070596894672413 chr5 180915260 89874514 0.4967768556394856 18.854328301796944 chr6 171115067 97733446 0.5711562851446623 15.348097235143696 chr7 159138663 72411652 0.4550223725330657 16.591170095570167 chr8 146364022 54663949 0.37347941285734826 12.717057235724697 chr9 141213431 84911578 0.6012995888471827 15.921073129680519 chr10 135534747 39866616 0.2941431395448726 9.91319110026623 chr11 135006516 64535085 0.4780145944955723 14.497671376393255 chr12 133851895 84877647 0.6341161400815432 18.979611661241403 chr13 115169878 37055921 0.3217501107364202 11.903671352794289 chr14 107349540 38955849 0.36288789872783805 14.845406654710882 chr15 102531392 44839494 0.4373245415413847 16.72066254626391 chr16 90354753 51338364 0.568186645366625 15.670123960996376 chr17 81195210 58099950 0.7155588365372785 17.339809525663153 chr18 78077248 38375212 0.491503132897307 16.88658612740578 chr19 59128983 23549474 0.39827294171455646 13.290958462751416 chr20 63025520 31122782 0.49381237949325923 16.18859635632069 chr21 48129895 7048423 0.14644584202811994 5.332707044095369 chr22 51304566 12601070 0.2456130317913614 6.907110460567205 chrMT 16571 1579 0.09528694707621749 0.35596526764221575 chrX 155270560 109274988 0.7037714554516967 31.97278095353708 chrY 59373566 4211850 0.070938134320583 4.257045293298074