BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085024.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 = 2,394,457 number of mapped reads = 2,176,881 (90.91%) number of supplementary alignments = 15,142 (0.63%) number of secondary alignments = 0 number of mapped bases = 145,725,755 bp number of sequenced bases = 145,673,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,172 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1365 >>>>>>> ACTG content number of A's = 40,899,266 bp (28.08%) number of C's = 28,292,736 bp (19.42%) number of T's = 44,629,083 bp (30.64%) number of G's = 31,836,169 bp (21.85%) number of N's = 16,120 bp (0.01%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,252,549 number of insertions = 9,820 mapped reads with insertion percentage = 0.45% number of deletions = 30,123 mapped reads with deletion percentage = 1.37% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.3371X There is a 3.83% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15766141 0.06325416938479764 0.5017040341963337 chr2 243199373 11316870 0.04653330253446007 0.3815618823001901 chr3 198022430 9491007 0.047928949260949885 0.26018019394202974 chr4 191154276 8747101 0.04575937919379842 0.2558378413746945 chr5 180915260 7447049 0.041163188776889244 0.24107935441792816 chr6 171115067 10706164 0.06256704443215395 0.33847833283438983 chr7 159138663 13312932 0.08365617599790945 0.45921365616203424 chr8 146364022 8830757 0.06033420562875759 0.518932014916336 chr9 141213431 3473663 0.024598672912352085 0.2529004280901789 chr10 135534747 9014044 0.0665072551469034 0.40632258856318937 chr11 135006516 7252497 0.05371960713362902 0.36817728918437626 chr12 133851895 6521779 0.04872384511254024 0.26673557468219516 chr13 115169878 3408267 0.029593388993604735 0.20189778017391555 chr14 107349540 3798731 0.035386560575853425 0.22837012761224157 chr15 102531392 2615437 0.025508646171506187 0.19200991004273094 chr16 90354753 3319158 0.03673473602434617 0.2334466515496722 chr17 81195210 2208680 0.027202097266575208 0.22004783477992007 chr18 78077248 4877544 0.062470746919768484 0.461402808874804 chr19 59128983 2348601 0.03971996271270216 0.34422416249110355 chr20 63025520 3363904 0.05337368101048591 0.27591709344654425 chr21 48129895 1187877 0.024680648067069332 0.19527735623910397 chr22 51304566 990126 0.019298984031947564 0.16135817765034022 chrMT 16571 12394 0.7479331362017984 1.148173906504719 chrX 155270560 5435946 0.03500950856363241 0.24681346020483022 chrY 59373566 279086 0.004700509314195479 0.09841815563811475