BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084775.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 = 1,595,123 number of mapped reads = 1,323,355 (82.96%) number of supplementary alignments = 12,796 (0.8%) number of secondary alignments = 0 number of mapped bases = 89,437,280 bp number of sequenced bases = 89,397,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,876 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9114 >>>>>>> ACTG content number of A's = 24,613,635 bp (27.53%) number of C's = 16,827,655 bp (18.82%) number of T's = 27,989,870 bp (31.31%) number of G's = 19,933,363 bp (22.3%) number of N's = 32,632 bp (0.04%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 803,717 number of insertions = 7,004 mapped reads with insertion percentage = 0.53% number of deletions = 24,615 mapped reads with deletion percentage = 1.84% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2685X There is a 2.59% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7094842 0.02846469136781007 0.4507804555164069 chr2 243199373 7627917 0.031364871158611085 0.3163372154674406 chr3 198022430 6078294 0.030694977331608343 0.18956686665362657 chr4 191154276 5786760 0.030272720658364973 0.1985842306560522 chr5 180915260 5515477 0.030486521700822805 0.1899071322414926 chr6 171115067 5220332 0.03050772846321008 0.2180970363583145 chr7 159138663 4871439 0.030611285203520907 0.3418567560567275 chr8 146364022 4609223 0.03149150274102197 0.28706884772403746 chr9 141213431 3757437 0.026608212642322954 0.25616900010569815 chr10 135534747 4209051 0.03105514337220108 0.26130853820908173 chr11 135006516 4081272 0.03023018533416565 0.24852647380625736 chr12 133851895 4034792 0.030143704726780296 0.18995751818375153 chr13 115169878 2910812 0.025274073833784907 0.17256391270850824 chr14 107349540 2713614 0.025278301145957402 0.18327832272189307 chr15 102531392 2582728 0.025189631678852072 0.17563234703940875 chr16 90354753 2460093 0.027227045820157354 0.19477999199836143 chr17 81195210 2337633 0.02879028208683739 0.21017224192869516 chr18 78077248 2455410 0.031448470110012075 0.5006206219216236 chr19 59128983 1701678 0.028779084531184985 0.33496260173216247 chr20 63025520 1858593 0.029489530590148246 0.19795515139659023 chr21 48129895 1181374 0.02454553453731823 0.1772782390285402 chr22 51304566 986589 0.019230042799699348 0.148514796076141 chrMT 16571 3904 0.2355922998008569 0.5415408390582702 chrX 155270560 5132451 0.03305488819000846 0.2168957677812006 chrY 59373566 225565 0.0037990812274944037 0.0968882441240626