BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971315.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,913,884 number of mapped reads = 11,653,009 (90.24%) number of supplementary alignments = 1,616 (0.01%) number of secondary alignments = 0 number of mapped bases = 559,034,799 bp number of sequenced bases = 558,913,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,262,480 duplication rate = 9.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2554 >>>>>>> ACTG content number of A's = 158,948,914 bp (28.44%) number of C's = 116,591,041 bp (20.86%) number of T's = 162,967,146 bp (29.16%) number of G's = 120,376,064 bp (21.54%) number of N's = 29,951 bp (0.01%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 2,568,675 number of insertions = 34,673 mapped reads with insertion percentage = 0.3% number of deletions = 83,213 mapped reads with deletion percentage = 0.71% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.1806X std coverageData = 1.4119X There is a 10.81% of reference with a coverageData >= 1X There is a 3.99% of reference with a coverageData >= 2X There is a 1.58% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 44820965 0.17982288196585877 2.3924100433694777 chr2 243199373 48463754 0.19927581803428415 1.2594687792453982 chr3 198022430 38349471 0.19366225836133816 0.6817764915600761 chr4 191154276 37351870 0.1954016974226619 0.8933438373214238 chr5 180915260 35572437 0.19662485630012635 0.6891513237302503 chr6 171115067 31901121 0.18643081266479006 0.7356645989920787 chr7 159138663 31541667 0.19820241294851146 1.7480403351931668 chr8 146364022 28415378 0.19414182263999277 3.33324842915075 chr9 141213431 23791494 0.168478974213154 1.134622316951019 chr10 135534747 27139893 0.2002430638690756 1.5956750047942387 chr11 135006516 25500479 0.18888332026877874 1.0381995075684927 chr12 133851895 26046502 0.1945919555341372 0.6988144062056718 chr13 115169878 17645411 0.15321203170849934 0.5901447687812447 chr14 107349540 16875597 0.1572023224319359 0.754302808093096 chr15 102531392 16077667 0.15680726347692617 0.6013259196108324 chr16 90354753 15858857 0.17551768416654295 0.8157899627859937 chr17 81195210 15158820 0.1866959885934158 0.7731428122296813 chr18 78077248 17086091 0.21883572279596739 2.201186755373036 chr19 59128983 12150926 0.20549864691567585 2.060422890499678 chr20 63025520 11477310 0.18210575652529323 0.6975237030047479 chr21 48129895 7197121 0.14953535635180587 0.8714176147091762 chr22 51304566 6306807 0.12292876622326364 0.6505713430941498 chrMT 16571 188507 11.37571661336069 8.223864807640224 chrX 155270560 19182874 0.12354482395117271 0.685616805014552 chrY 59373566 4933780 0.08309724903503354 0.8384600213937967