BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505985.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,745,778 number of mapped reads = 4,815,274 (71.38%) number of supplementary alignments = 263 (0%) number of secondary alignments = 0 number of mapped bases = 223,277,943 bp number of sequenced bases = 223,235,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 428,816 duplication rate = 6.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1642 >>>>>>> ACTG content number of A's = 65,049,292 bp (29.14%) number of C's = 46,181,741 bp (20.69%) number of T's = 65,073,983 bp (29.15%) number of G's = 46,929,833 bp (21.02%) number of N's = 865 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,110,199 number of insertions = 10,399 mapped reads with insertion percentage = 0.22% number of deletions = 30,763 mapped reads with deletion percentage = 0.64% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 0.0721X std coverageData = 0.5742X There is a 5.21% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18527911 0.0743344627414188 1.0756702088351906 chr2 243199373 18844569 0.07748609203856788 0.5017440923575102 chr3 198022430 14984460 0.07567051873871056 0.36396781921309174 chr4 191154276 14734982 0.07708423953853902 0.38204157489877516 chr5 180915260 13915138 0.07691522539336924 0.37249313028603415 chr6 171115067 12557469 0.07338610924308611 0.42210033986797213 chr7 159138663 12681172 0.07968630476680579 0.7383990882835485 chr8 146364022 11453157 0.07825117705497325 0.9766055101553095 chr9 141213431 9221564 0.06530231533004817 0.44550182990321824 chr10 135534747 10627947 0.07841492484580356 0.571639794884241 chr11 135006516 10308756 0.07635747003500186 0.5025115687401326 chr12 133851895 10228823 0.07641896291419707 0.39679153048768456 chr13 115169878 6576134 0.05709942664001085 0.31332638299689275 chr14 107349540 6965284 0.064884153206432 0.4374345014249396 chr15 102531392 6192856 0.06039960912653951 0.3226529679579256 chr16 90354753 6032351 0.06676296265233551 0.3785349356466113 chr17 81195210 5886747 0.0725011610906604 0.3986994612502313 chr18 78077248 5737847 0.07348936017826858 0.8297496013834649 chr19 59128983 4462695 0.07547390084486993 0.7588742424705457 chr20 63025520 4646092 0.07371763057250459 0.37821930151824035 chr21 48129895 2870368 0.05963794435869848 0.356351213814433 chr22 51304566 2510277 0.04892891989379659 0.2941006767525275 chrMT 16571 41968 2.532617222859212 2.5480687194880964 chrX 155270560 12568792 0.08094768254844963 0.43179658636513063 chrY 59373566 700584 0.011799594452521177 0.1962280581163085