BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926936.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 = 12,615,168 number of mapped reads = 12,273,290 (97.29%) number of supplementary alignments = 437,175 (3.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,142,684 number of mapped paired reads (second in pair) = 6,130,606 number of mapped paired reads (both in pair) = 12,085,490 number of mapped paired reads (singletons) = 187,800 number of mapped bases = 1,124,778,231 bp number of sequenced bases = 1,123,925,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 746,274 duplication rate = 4.89% >>>>>>> Insert size mean insert size = 360,542.7063 std insert size = 5,907,463.0739 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.6389 >>>>>>> ACTG content number of A's = 318,967,045 bp (28.38%) number of C's = 223,224,829 bp (19.86%) number of T's = 323,046,854 bp (28.74%) number of G's = 258,632,181 bp (23.01%) number of N's = 55,079 bp (0%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 10,005,002 number of insertions = 193,731 mapped reads with insertion percentage = 1.55% number of deletions = 567,804 mapped reads with deletion percentage = 4.51% homopolymer indels = 51.98% >>>>>>> Coverage mean coverageData = 0.3633X std coverageData = 1.4833X There is a 20.83% of reference with a coverageData >= 1X There is a 8.43% of reference with a coverageData >= 2X There is a 3.42% of reference with a coverageData >= 3X There is a 1.56% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 97394620 0.3907497586535602 1.7174757663149596 chr2 243199373 99334055 0.4084470028629556 2.8173680679120654 chr3 198022430 78479571 0.39631657383459035 0.9475116955997034 chr4 191154276 63978428 0.33469524898307795 1.2395581720901243 chr5 180915260 66525075 0.3677140059937454 0.8929442848255346 chr6 171115067 63942949 0.37368391995545314 1.0323008847578814 chr7 159138663 61195046 0.38453914872968364 1.0470701382407992 chr8 146364022 60103059 0.4106409360628256 1.0302188655305173 chr9 141213431 46666345 0.3304667599217244 1.5087820517115222 chr10 135534747 52010026 0.3837394258757867 2.4521287029025496 chr11 135006516 53069648 0.3930895305823609 1.2476638929815334 chr12 133851895 50044511 0.3738797347620667 0.9535083507123789 chr13 115169878 34263807 0.2975066709717275 0.8056939807556316 chr14 107349540 33447369 0.31157440451072266 0.8646340083600392 chr15 102531392 33964742 0.331261883189882 0.890144736985128 chr16 90354753 36044243 0.3989191691996546 2.3519437644634626 chr17 81195210 28445749 0.3503377723882973 1.0321231843003749 chr18 78077248 27420985 0.35120327243091354 1.5225804301974337 chr19 59128983 17944704 0.30348406296790187 1.231591892699195 chr20 63025520 25382650 0.4027360662791834 1.0087626223227266 chr21 48129895 14027595 0.29145284858818 1.192302407538784 chr22 51304566 13767825 0.2683547698269195 0.8727686519384394 chrMT 16571 18244 1.1009595075734717 1.441032960836913 chrX 155270560 65187872 0.41983407543580703 1.0475554152910054 chrY 59373566 2119113 0.03569118620902777 1.3187755147551126