BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238518.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,566,354 number of mapped reads = 5,000,143 (89.83%) number of supplementary alignments = 35,474 (0.64%) number of secondary alignments = 0 number of mapped bases = 309,924,131 bp number of sequenced bases = 309,771,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,377,811 duplication rate = 19.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3434 >>>>>>> ACTG content number of A's = 74,575,775 bp (24.07%) number of C's = 55,463,363 bp (17.9%) number of T's = 103,882,408 bp (33.54%) number of G's = 75,828,895 bp (24.48%) number of N's = 20,959 bp (0.01%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,891,865 number of insertions = 20,714 mapped reads with insertion percentage = 0.41% number of deletions = 91,129 mapped reads with deletion percentage = 1.8% homopolymer indels = 40.64% >>>>>>> Coverage mean coverageData = 0.1001X std coverageData = 1.6419X There is a 4.77% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 22397182 0.08985807902962055 1.6636014892021662 chr2 243199373 22006589 0.09048785253241587 4.560267185245351 chr3 198022430 14082670 0.07111653967684368 0.5375251020349938 chr4 191154276 8713356 0.045582846391571175 0.41632376127027393 chr5 180915260 22101781 0.12216648280526474 0.6870933355334963 chr6 171115067 18400036 0.10753019194972468 1.436231864506737 chr7 159138663 24399464 0.1533220371469377 1.828116012558659 chr8 146364022 23367701 0.15965467934462746 1.040046992849979 chr9 141213431 7050522 0.04992812617094475 0.8051472324987811 chr10 135534747 22303642 0.1645603248884952 0.8981578856150344 chr11 135006516 9623639 0.07128277423291184 0.5762877293835591 chr12 133851895 9877986 0.07379787936509977 0.5430059867428484 chr13 115169878 6667669 0.057894209109086665 0.853335257820197 chr14 107349540 5562434 0.051816095346100224 0.46573393965658727 chr15 102531392 7958644 0.07762153468081268 0.9053986714192132 chr16 90354753 11908110 0.13179284547432718 0.8137671694560059 chr17 81195210 8958364 0.11033118825605599 0.6331607788659709 chr18 78077248 18465777 0.23650650443007418 2.682912495456126 chr19 59128983 8079728 0.1366458137796823 1.1103210406888193 chr20 63025520 13104604 0.20792536102835804 0.904370238689732 chr21 48129895 7961999 0.1654273087443885 0.8363667198958071 chr22 51304566 4231342 0.0824749594412318 0.5474783365393936 chrMT 16571 25208 1.5212117554764348 2.220944394992952 chrX 155270560 12023387 0.0774350720445653 0.5764422979241108 chrY 59373566 652297 0.010986320073818709 0.5339291939695371