BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617385.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,967,218 (93.65%) number of supplementary alignments = 98,637 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,127,986 number of mapped paired reads (second in pair) = 14,839,232 number of mapped paired reads (both in pair) = 29,297,022 number of mapped paired reads (singletons) = 670,196 number of mapped bases = 2,932,256,420 bp number of sequenced bases = 2,931,386,270 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,578,442 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 70,398.5205 std insert size = 2,543,943.2599 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 53.3465 >>>>>>> ACTG content number of A's = 888,051,045 bp (30.29%) number of C's = 581,655,248 bp (19.84%) number of T's = 876,247,647 bp (29.89%) number of G's = 584,531,239 bp (19.94%) number of N's = 901,091 bp (0.03%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 31,719,529 number of insertions = 301,793 mapped reads with insertion percentage = 0.98% number of deletions = 360,346 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.2% >>>>>>> Coverage mean coverageData = 0.9472X std coverageData = 9.5916X There is a 52.8% of reference with a coverageData >= 1X There is a 23.63% of reference with a coverageData >= 2X There is a 8.98% of reference with a coverageData >= 3X There is a 3.12% of reference with a coverageData >= 4X There is a 1.06% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190475983 0.76419461759335 19.53597824789423 chr2 243199373 289540004 1.1905458489812801 8.65550865784804 chr3 198022430 233614336 1.179736739923856 1.4809753388356945 chr4 191154276 160584462 0.84007779140656 9.233247541511835 chr5 180915260 184090785 1.0175525547153954 1.4425088508790695 chr6 171115067 137568686 0.8039542537770797 3.6036999063424013 chr7 159138663 238274858 1.4972782446965764 10.776162100165996 chr8 146364022 123397176 0.8430840743089173 7.564074212298586 chr9 141213431 123559017 0.8749806312687071 14.45319245506373 chr10 135534747 123352297 0.910115669452646 19.575000339932938 chr11 135006516 157417162 1.1659967730742715 5.4577931879677095 chr12 133851895 129376903 0.9665675857633543 1.393030588756877 chr13 115169878 127633556 1.1082199461911386 1.331008502011937 chr14 107349540 84708825 0.7890935070611388 1.3590115084730894 chr15 102531392 65885687 0.6425903883173653 1.1284529361735023 chr16 90354753 73799053 0.8167700154080438 7.735811127201041 chr17 81195210 91253076 1.1238726520936395 7.021276042863758 chr18 78077248 52898427 0.6775139794886214 15.096376287732662 chr19 59128983 54384380 0.9197584203333922 9.297491673786503 chr20 63025520 83799518 1.3296124807855612 2.4107939367750584 chr21 48129895 46595167 0.9681127914365905 3.1823271039735235 chr22 51304566 26063677 0.5080186625104673 0.9256051252407491 chrMT 16571 1993252 120.2855591092873 20.91149963210373 chrX 155270560 121917716 0.7851953132647941 2.9623282307846304 chrY 59373566 10072417 0.16964480455831135 8.232353054743502