BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708555.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,377,755 number of mapped reads = 3,612,636 (82.52%) number of supplementary alignments = 110 (0%) number of secondary alignments = 0 number of mapped bases = 180,154,102 bp number of sequenced bases = 180,137,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,160 duplication rate = 0.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5523 >>>>>>> ACTG content number of A's = 55,645,631 bp (30.89%) number of C's = 34,328,405 bp (19.06%) number of T's = 55,460,081 bp (30.79%) number of G's = 34,698,559 bp (19.26%) number of N's = 5,065 bp (0%) GC percentage = 38.32% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 285,427 number of insertions = 11,922 mapped reads with insertion percentage = 0.33% number of deletions = 9,718 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.2485X There is a 5.49% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 13656623 0.05479072808408369 0.241989439329407 chr2 243199373 15362746 0.06316934871374032 0.25785503233831814 chr3 198022430 13438875 0.06786541807410403 0.26719893836877334 chr4 191154276 13430507 0.07026003959231339 0.2720832419847511 chr5 180915260 12494051 0.06906023847850093 0.269496108355205 chr6 171115067 11319400 0.06615080833296813 0.26371636460747483 chr7 159138663 9649061 0.06063304050757295 0.25335792875854324 chr8 146364022 9747346 0.0665965984454841 0.2648939438138689 chr9 141213431 7641877 0.054115794410518926 0.2403852023345184 chr10 135534747 7740782 0.05711289666553183 0.24528829707148214 chr11 135006516 8465605 0.06270515861619598 0.25890120844203085 chr12 133851895 8286795 0.0619101806515328 0.2561484571754728 chr13 115169878 7096048 0.061613749386797124 0.2557843061305299 chr14 107349540 5716831 0.05325435954359935 0.23826609048690703 chr15 102531392 5075096 0.04949797228930628 0.2305214492689629 chr16 90354753 3571003 0.0395220271367462 0.20470133543326077 chr17 81195210 3141655 0.03869261499539197 0.2027110041490767 chr18 78077248 5019381 0.06428737088684273 0.2602069688461425 chr19 59128983 1628025 0.027533451742269947 0.16979996531466696 chr20 63025520 2980876 0.04729633329483041 0.22394797107013206 chr21 48129895 2245765 0.046660500713745584 0.22408647105234455 chr22 51304566 1014629 0.01977658284839599 0.14373934047155304 chrMT 16571 350 0.021121235894031743 0.17065644917773576 chrX 155270560 11151764 0.07182149661854766 0.2760283101758697 chrY 59373566 279011 0.0046992461257927476 0.07141924800123282