BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081219.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 = 2,552,641 number of mapped reads = 2,254,417 (88.32%) number of supplementary alignments = 27,404 (1.07%) number of secondary alignments = 0 number of mapped bases = 146,848,716 bp number of sequenced bases = 146,793,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,256 duplication rate = 4.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3271 >>>>>>> ACTG content number of A's = 41,898,440 bp (28.54%) number of C's = 28,492,939 bp (19.41%) number of T's = 44,852,660 bp (30.55%) number of G's = 31,530,189 bp (21.48%) number of N's = 19,272 bp (0.01%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,313,956 number of insertions = 10,947 mapped reads with insertion percentage = 0.48% number of deletions = 33,471 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.3388X There is a 3.78% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.15% 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 15137617 0.06073251468448698 0.5334589999629087 chr2 243199373 9390958 0.03861423606548525 0.35972233618448385 chr3 198022430 9276665 0.046846536526190495 0.2636779301051213 chr4 191154276 6794264 0.03554335347434237 0.23211476027232095 chr5 180915260 7938017 0.04387698970225066 0.25331777575778974 chr6 171115067 10436641 0.060991946430994294 0.32609130745784054 chr7 159138663 9708094 0.06100399373092634 0.46129054343318066 chr8 146364022 9224807 0.06302646561598314 0.41541946794303614 chr9 141213431 4308592 0.03051120541076578 0.2646863165615046 chr10 135534747 4759077 0.03511333518038736 0.31317356769064636 chr11 135006516 8282121 0.061346083473482124 0.3970151918079704 chr12 133851895 4700823 0.035119584971135445 0.22753433386740696 chr13 115169878 4035944 0.03504339910822863 0.2277227414221582 chr14 107349540 5915235 0.05510256494811249 0.2951228816840424 chr15 102531392 2436964 0.02376797927409393 0.18878997094277689 chr16 90354753 5530436 0.06120802521589539 0.3072560447320949 chr17 81195210 2644048 0.03256408844807471 0.23319378995094955 chr18 78077248 4019514 0.05148124585538671 0.427379395855931 chr19 59128983 4040266 0.0683297055861759 0.4643173837260347 chr20 63025520 3623820 0.057497661264833674 0.29590430641518517 chr21 48129895 2491530 0.0517667865263367 0.2834892992171031 chr22 51304566 1147996 0.022376098065033823 0.17931746020833117 chrMT 16571 38002 2.293283446985698 2.2573833270372505 chrX 155270560 10604399 0.06829626298765201 0.3316472080870894 chrY 59373566 362886 0.006111911822847225 0.1095943299103013