BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081962.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 = 3,130,415 number of mapped reads = 2,835,545 (90.58%) number of supplementary alignments = 18,812 (0.6%) number of secondary alignments = 0 number of mapped bases = 190,113,294 bp number of sequenced bases = 190,041,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,489 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8461 >>>>>>> ACTG content number of A's = 52,912,938 bp (27.84%) number of C's = 35,032,674 bp (18.43%) number of T's = 60,098,675 bp (31.62%) number of G's = 41,973,128 bp (22.09%) number of N's = 23,885 bp (0.01%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,466,123 number of insertions = 13,596 mapped reads with insertion percentage = 0.48% number of deletions = 41,055 mapped reads with deletion percentage = 1.43% homopolymer indels = 48.42% >>>>>>> Coverage mean coverageData = 0.0614X std coverageData = 0.4934X There is a 5.04% of reference with a coverageData >= 1X There is a 0.79% 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 0.01% 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 17723139 0.0711056964628385 0.8892387115560572 chr2 243199373 16865118 0.06934688108755939 0.7272665256250334 chr3 198022430 11796159 0.05956981236923514 0.2848086916779188 chr4 191154276 9059735 0.04739488537520343 0.2687270109630102 chr5 180915260 10436668 0.05768815742795826 0.28105119930298583 chr6 171115067 15999533 0.09350160263794888 0.44307670466379373 chr7 159138663 13464204 0.08460674324001327 0.6278241477012863 chr8 146364022 9785220 0.06685536422331985 0.5781249261839212 chr9 141213431 8820056 0.06245904470659027 0.5085491728686948 chr10 135534747 7467109 0.05509368752501526 0.43421558258910375 chr11 135006516 8334419 0.061733457368828036 0.40184162473686685 chr12 133851895 8398921 0.06274786770855953 0.2993876023623925 chr13 115169878 5238059 0.045481154369200597 0.25109892122752275 chr14 107349540 4708702 0.043863271328409975 0.26784868748458585 chr15 102531392 4354966 0.042474464796108495 0.24717920651185296 chr16 90354753 3740661 0.04139971474439203 0.27059648290723953 chr17 81195210 5117992 0.0630331764644737 0.32446214459439376 chr18 78077248 5273306 0.06753959873175858 0.7565801776595358 chr19 59128983 4384720 0.0741551736142663 0.6503074921796385 chr20 63025520 5177090 0.08214275741001423 0.34519093190038364 chr21 48129895 1996579 0.04148313641656604 0.2620687708252985 chr22 51304566 1601187 0.031209444399159326 0.2038879008655049 chrMT 16571 216695 13.076760605877737 7.606370362614322 chrX 155270560 9742196 0.06274335585573981 0.3381084153875197 chrY 59373566 410860 0.0069199144952822944 0.1450275302563902