BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081158.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 = 2,488,690 number of mapped reads = 2,260,008 (90.81%) number of supplementary alignments = 25,219 (1.01%) number of secondary alignments = 0 number of mapped bases = 152,725,568 bp number of sequenced bases = 152,667,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,407 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2266 >>>>>>> ACTG content number of A's = 43,783,419 bp (28.68%) number of C's = 28,257,991 bp (18.51%) number of T's = 47,993,368 bp (31.44%) number of G's = 32,586,862 bp (21.34%) number of N's = 45,920 bp (0.03%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,251,206 number of insertions = 11,889 mapped reads with insertion percentage = 0.52% number of deletions = 35,765 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.3773X There is a 4.21% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11895575 0.04772535752278025 0.6015790788410308 chr2 243199373 13400754 0.0551019265991282 0.42801832792836303 chr3 198022430 10158181 0.05129813324682461 0.2554837896560408 chr4 191154276 10299512 0.05388062572034748 0.2703821076346427 chr5 180915260 10270019 0.056767013462545944 0.2703227394466726 chr6 171115067 8813019 0.0515034657935762 0.3494543485491431 chr7 159138663 8105350 0.050932625970346375 0.4303903873587124 chr8 146364022 7691807 0.052552580168916105 0.6046519881571735 chr9 141213431 6184956 0.043798638388723804 0.3492145719637165 chr10 135534747 7158551 0.05281709051332792 0.3271847296777444 chr11 135006516 6421334 0.04756314132274919 0.32205649732153285 chr12 133851895 7117947 0.05317778280240261 0.2659931735495887 chr13 115169878 5469694 0.04749240074735514 0.2464793836869845 chr14 107349540 4615160 0.042991893584266874 0.25269969712660834 chr15 102531392 3918635 0.038218880321063034 0.22775656191461596 chr16 90354753 3652892 0.04042833253055321 0.2644255464027832 chr17 81195210 3756506 0.04626511834873018 0.26924199250132 chr18 78077248 4091772 0.05240671392516293 0.6859113952338137 chr19 59128983 2471081 0.04179136651141117 0.43892129150484893 chr20 63025520 2838287 0.04503393228647697 0.24709710695605971 chr21 48129895 1873703 0.038930128561468914 0.23859372721443106 chr22 51304566 1480631 0.028859634052844342 0.18984437486223132 chrMT 16571 10957 0.6612153762597308 0.9931289841038642 chrX 155270560 10645211 0.06855910740580828 0.33640234110766687 chrY 59373566 384034 0.006468097267393371 0.11766673435740352