BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926906.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,865,384 number of mapped reads = 28,012,864 (97.05%) number of supplementary alignments = 1,249,539 (4.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,012,539 number of mapped paired reads (second in pair) = 14,000,325 number of mapped paired reads (both in pair) = 27,645,202 number of mapped paired reads (singletons) = 367,662 number of mapped bases = 2,546,905,268 bp number of sequenced bases = 2,544,863,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,743,252 duplication rate = 7.62% >>>>>>> Insert size mean insert size = 488,636.8559 std insert size = 6,883,332.3282 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.1054 >>>>>>> ACTG content number of A's = 717,951,620 bp (28.21%) number of C's = 505,777,556 bp (19.87%) number of T's = 724,448,151 bp (28.47%) number of G's = 596,398,762 bp (23.44%) number of N's = 287,510 bp (0.01%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 24,971,842 number of insertions = 448,147 mapped reads with insertion percentage = 1.57% number of deletions = 1,373,641 mapped reads with deletion percentage = 4.78% homopolymer indels = 51.48% >>>>>>> Coverage mean coverageData = 0.8227X std coverageData = 3.6333X There is a 32.83% of reference with a coverageData >= 1X There is a 18.08% of reference with a coverageData >= 2X There is a 10.31% of reference with a coverageData >= 3X There is a 6.38% of reference with a coverageData >= 4X There is a 4.09% of reference with a coverageData >= 5X There is a 2.71% of reference with a coverageData >= 6X There is a 1.84% of reference with a coverageData >= 7X There is a 1.28% of reference with a coverageData >= 8X There is a 0.9% of reference with a coverageData >= 9X There is a 0.65% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 210327131 0.843837941731748 2.636894205742996 chr2 243199373 218893172 0.9000564816423272 5.455865075376694 chr3 198022430 170405567 0.8605366927372823 1.9783750580365145 chr4 191154276 148896236 0.7789322798094247 2.0344017393389158 chr5 180915260 152237708 0.8414862737394292 1.7666201345705401 chr6 171115067 143599934 0.8392009921604391 1.7742083126486523 chr7 159138663 130331685 0.8189819025939661 2.17019200190545 chr8 146364022 128174921 0.875726966562862 1.9753858644318587 chr9 141213431 110437275 0.7820592858479588 3.3394951934230863 chr10 135534747 129787758 0.9575976705073276 11.540709691208702 chr11 135006516 121961351 0.9033738119721569 2.441613476823371 chr12 133851895 115266052 0.8611462093980814 1.904319355361194 chr13 115169878 75160764 0.6526078285851792 1.5528108639056313 chr14 107349540 76507179 0.7126921922534554 1.6888280626202805 chr15 102531392 76041918 0.7416452319305291 1.7472550699766367 chr16 90354753 83511227 0.9242593690671702 5.352714867919521 chr17 81195210 68228074 0.8402967859803553 2.0086883765197996 chr18 78077248 66314452 0.8493441264733101 3.2513450384010993 chr19 59128983 44552802 0.7534850041307154 2.0391906640149924 chr20 63025520 60765846 0.9641466821693816 2.075990133632679 chr21 48129895 32236993 0.6697914674445061 2.5622127442267573 chr22 51304566 33327804 0.6496069765018575 1.7643142856405511 chrMT 16571 2311260 139.476193349828 92.27518811973776 chrX 155270560 143351893 0.9232393635986114 1.9512756418479607 chrY 59373566 4276266 0.07202306157592084 2.0597946779856113