BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082947.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 = 1,736,141 number of mapped reads = 1,588,385 (91.49%) number of supplementary alignments = 16,243 (0.94%) number of secondary alignments = 0 number of mapped bases = 106,658,601 bp number of sequenced bases = 106,616,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,211 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9642 >>>>>>> ACTG content number of A's = 29,586,058 bp (27.75%) number of C's = 19,347,548 bp (18.15%) number of T's = 34,304,013 bp (32.18%) number of G's = 23,374,357 bp (21.92%) number of N's = 4,971 bp (0%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 785,606 number of insertions = 8,712 mapped reads with insertion percentage = 0.54% number of deletions = 25,685 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.3318X There is a 2.95% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% 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 10551210 0.04233173003809688 0.6574188662940783 chr2 243199373 11388965 0.046829746555308756 0.4342865478713776 chr3 198022430 7371981 0.03722800997846557 0.2162248687657503 chr4 191154276 5791289 0.030296413562833406 0.202108539524251 chr5 180915260 6102546 0.03373151607000979 0.2079250485299746 chr6 171115067 7022850 0.04104168103443515 0.30096460117016255 chr7 159138663 5202305 0.03269039026675749 0.28479926417775264 chr8 146364022 9848021 0.06728443824808258 0.4736100340230394 chr9 141213431 3459440 0.02449795303111076 0.2803556317831375 chr10 135534747 3814840 0.028146582957062665 0.22683410770641474 chr11 135006516 4567984 0.03383528540207645 0.2797229954573423 chr12 133851895 3404010 0.025431167784363457 0.1866044756017465 chr13 115169878 2013353 0.0174815935812661 0.15180657323007168 chr14 107349540 2431285 0.022648303849275925 0.19196184562665786 chr15 102531392 2114999 0.020627819039070492 0.16840153027996949 chr16 90354753 4014927 0.04443514996936575 0.25116690046904827 chr17 81195210 2417043 0.029768295445014553 0.22513017322124604 chr18 78077248 3569012 0.04571129351280414 0.5734088302266813 chr19 59128983 1757528 0.029723629780677947 0.36752781143734653 chr20 63025520 2119499 0.033629218767254915 0.21638841153924146 chr21 48129895 2019729 0.04196412645404691 0.23522517199176507 chr22 51304566 1345426 0.026224293564826178 0.18042644068965602 chrMT 16571 56370 3.401725906704484 2.523139532545567 chrX 155270560 4088269 0.026329968797690947 0.20541442487919168 chrY 59373566 185720 0.003127991335403368 0.07369016082488142