BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083787.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,520,377 number of mapped reads = 1,923,249 (76.31%) number of supplementary alignments = 10,903 (0.43%) number of secondary alignments = 0 number of mapped bases = 123,045,903 bp number of sequenced bases = 123,004,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,705 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4622 >>>>>>> ACTG content number of A's = 34,397,520 bp (27.96%) number of C's = 23,578,664 bp (19.17%) number of T's = 37,275,237 bp (30.3%) number of G's = 27,751,231 bp (22.56%) number of N's = 1,415 bp (0%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,022,512 number of insertions = 9,298 mapped reads with insertion percentage = 0.48% number of deletions = 25,960 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.83% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.2857X There is a 3.49% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 9778969 0.03923347898098115 0.364418918520953 chr2 243199373 10392463 0.042732277109941395 0.38517758928956125 chr3 198022430 8389177 0.04236478160580092 0.228036855126526 chr4 191154276 7946134 0.04156921919967932 0.2327377462375619 chr5 180915260 7604423 0.04203306564631419 0.2283289695073838 chr6 171115067 7393627 0.04320850951132199 0.2638216318232264 chr7 159138663 6551149 0.0411662940765061 0.33096136818593586 chr8 146364022 6308543 0.04310173302015437 0.3042858060242304 chr9 141213431 5000929 0.03541397560123017 0.28001448759789854 chr10 135534747 5747437 0.04240563491810701 0.2777612011329354 chr11 135006516 5662400 0.04194167931864859 0.2685240801526418 chr12 133851895 5570002 0.041613172529234646 0.22876597897463652 chr13 115169878 4005662 0.03478046577421919 0.208970801270884 chr14 107349540 3749047 0.03492373604954432 0.21889062607087814 chr15 102531392 3504900 0.034183677131780284 0.21346631017121082 chr16 90354753 3455570 0.03824447397913865 0.2351126012080589 chr17 81195210 3204343 0.03946468024406859 0.23710036971372564 chr18 78077248 3260719 0.04176272964948764 0.5284359714144891 chr19 59128983 2292408 0.03876961658549074 0.31528846296444546 chr20 63025520 2561395 0.04064060082328555 0.22978487265835248 chr21 48129895 1700968 0.03534119490599346 0.21886782595393847 chr22 51304566 1362086 0.026549020997468333 0.17981411596464947 chrMT 16571 143443 8.656266972421701 5.661945702366442 chrX 155270560 7165840 0.046150667583088514 0.259151860507173 chrY 59373566 294269 0.0049562291744443985 0.09964586586625107