BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080705.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 = 1,981,303 number of mapped reads = 1,686,150 (85.1%) number of supplementary alignments = 18,170 (0.92%) number of secondary alignments = 0 number of mapped bases = 114,981,306 bp number of sequenced bases = 114,939,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,454 duplication rate = 5.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1753 >>>>>>> ACTG content number of A's = 33,796,616 bp (29.4%) number of C's = 21,061,092 bp (18.32%) number of T's = 36,023,751 bp (31.34%) number of G's = 24,056,096 bp (20.93%) number of N's = 1,621 bp (0%) GC percentage = 39.25% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 937,949 number of insertions = 8,666 mapped reads with insertion percentage = 0.51% number of deletions = 23,894 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.0371X std coverageData = 0.3187X There is a 2.74% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 10547938 0.04231860268865689 0.396447004757774 chr2 243199373 9583008 0.039403917377698175 0.3312977671633567 chr3 198022430 7152008 0.036117161071096845 0.24490594678606087 chr4 191154276 8265976 0.04324243314337368 0.27614082043127025 chr5 180915260 7095380 0.03921935606758656 0.25625148603285175 chr6 171115067 6735070 0.039359888746675946 0.26799250004120934 chr7 159138663 6428401 0.04039496674670441 0.34529596565593723 chr8 146364022 6225995 0.042537741959564355 0.6642714073853204 chr9 141213431 4856564 0.03439165783033768 0.2880859909727721 chr10 135534747 5365401 0.03958690386606174 0.2805942704555613 chr11 135006516 5232921 0.038760506937309605 0.2784257780815346 chr12 133851895 5039125 0.037647020238301444 0.2532930803424452 chr13 115169878 3780446 0.032824954455539145 0.23522420985774295 chr14 107349540 3611872 0.03364590104438268 0.25056639806947584 chr15 102531392 3026622 0.02951897892891184 0.22217557883528696 chr16 90354753 2847628 0.03151608416216909 0.23744679933696136 chr17 81195210 2390398 0.0294401356927336 0.22380127840913058 chr18 78077248 2978455 0.03814754075348557 0.4332930930894706 chr19 59128983 1762921 0.0298148371670793 0.30075804704834647 chr20 63025520 2250692 0.035710804131405816 0.24667877333228477 chr21 48129895 1410948 0.029315418203177047 0.22906120187627607 chr22 51304566 1083222 0.021113559366236524 0.18336820433061812 chrMT 16571 239535 14.455072113933982 8.472385385311563 chrX 155270560 6800627 0.04379856039676807 0.2780244559828751 chrY 59373566 270153 0.0045500551541741655 0.1053938840820027