BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695935.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 11,655,238 number of mapped reads = 10,610,595 (91.04%) number of supplementary alignments = 25,976 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,365,537 number of mapped paired reads (second in pair) = 5,245,058 number of mapped paired reads (both in pair) = 10,222,882 number of mapped paired reads (singletons) = 387,713 number of mapped bases = 894,104,570 bp number of sequenced bases = 893,781,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,118,558 duplication rate = 6.65% >>>>>>> Insert size mean insert size = 65,403.8902 std insert size = 2,454,365.6218 median insert size = 282 >>>>>>> Mapping quality mean mapping quality = 52.4678 >>>>>>> ACTG content number of A's = 227,316,233 bp (25.43%) number of C's = 169,678,892 bp (18.98%) number of T's = 267,635,341 bp (29.94%) number of G's = 228,860,187 bp (25.61%) number of N's = 290,504 bp (0.03%) GC percentage = 44.59% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 13,692,550 number of insertions = 90,200 mapped reads with insertion percentage = 0.84% number of deletions = 215,401 mapped reads with deletion percentage = 2% homopolymer indels = 41.53% >>>>>>> Coverage mean coverageData = 0.2888X std coverageData = 3.6574X There is a 15.07% of reference with a coverageData >= 1X There is a 5.62% of reference with a coverageData >= 2X There is a 2.69% of reference with a coverageData >= 3X There is a 1.48% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% 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 0.02% 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 0.01% 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 0.01% 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% 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 73019112 0.29295458405297214 2.488549262629728 chr2 243199373 81793552 0.33632303813546427 6.985948283549487 chr3 198022430 60737497 0.3067202892116817 1.0190926778907743 chr4 191154276 54833086 0.28685252115416976 1.482375262637664 chr5 180915260 53925056 0.2980680347252078 1.3905407136713965 chr6 171115067 51748064 0.3024167591273538 4.2733303464521235 chr7 159138663 49864979 0.31334295550792707 4.603099802610086 chr8 146364022 48019379 0.3280818492402457 3.262666723999547 chr9 141213431 39470694 0.2795109057296398 5.201558682937857 chr10 135534747 44566076 0.3288166096624654 1.4360346958316152 chr11 135006516 43217429 0.3201136528847245 6.58194861383663 chr12 133851895 41861888 0.31274781727968815 1.3996403715665757 chr13 115169878 27267278 0.23675702773601964 0.886258597681062 chr14 107349540 27344946 0.254728115276507 1.9167642748788705 chr15 102531392 26046252 0.254031974909694 0.9454709232625181 chr16 90354753 26628132 0.2947064887665622 1.6313646114497768 chr17 81195210 24173770 0.29772408988165683 2.3864600845857376 chr18 78077248 26611095 0.3408303402292048 8.31035908613928 chr19 59128983 14046038 0.23754912206083437 1.4870454617399287 chr20 63025520 21064549 0.33422253398305957 1.2143570582159324 chr21 48129895 12324748 0.2560726134972869 3.0376808521482466 chr22 51304566 10384395 0.2024068384088855 0.8642744280174592 chrMT 16571 150782 9.099149115925412 22.939403031952224 chrX 155270560 28045293 0.18062208959637938 2.8736239308187725 chrY 59373566 6960480 0.11723196817923989 1.1582582240860009