BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975294.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,187,088 number of mapped reads = 5,152,065 (99.32%) number of supplementary alignments = 23,390 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,575,537 number of mapped paired reads (second in pair) = 2,576,528 number of mapped paired reads (both in pair) = 5,139,996 number of mapped paired reads (singletons) = 12,069 number of mapped bases = 489,494,624 bp number of sequenced bases = 489,205,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 263,798 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 69,678.3227 std insert size = 2,555,621.5043 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.1475 >>>>>>> ACTG content number of A's = 142,545,887 bp (29.14%) number of C's = 98,311,622 bp (20.1%) number of T's = 146,249,051 bp (29.9%) number of G's = 102,086,062 bp (20.87%) number of N's = 13,201 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 4,058,999 number of insertions = 76,929 mapped reads with insertion percentage = 1.47% number of deletions = 178,523 mapped reads with deletion percentage = 3.4% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.1581X std coverageData = 1.3211X There is a 10.74% of reference with a coverageData >= 1X There is a 3.22% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 45631047 0.18307295210309626 1.6347164843764883 chr2 243199373 42084250 0.1730442372480952 1.4462032635735849 chr3 198022430 35059537 0.17704831215332525 0.5757465973388906 chr4 191154276 29392532 0.15376340312680215 0.707608792809546 chr5 180915260 29317384 0.16205036545839197 0.5181958417334034 chr6 171115067 39357161 0.2300040650423846 1.27598955480746 chr7 159138663 29134920 0.18307882855594934 1.4131574736142958 chr8 146364022 24703366 0.16878031679123986 0.6606925121224618 chr9 141213431 20929472 0.1482116244311067 2.1879392703506273 chr10 135534747 25586470 0.18878162660384057 3.0228712246007574 chr11 135006516 17425868 0.12907427371875888 1.4291411104788068 chr12 133851895 21677138 0.161948682160981 0.5239020486232758 chr13 115169878 15694206 0.13627005839148323 0.47778070022582 chr14 107349540 14663270 0.1365936919711067 0.5170253581377843 chr15 102531392 14187487 0.13837212899635656 0.48275902753278793 chr16 90354753 15780016 0.17464511247128306 1.78639606648159 chr17 81195210 9824264 0.12099561045534582 1.176581617300538 chr18 78077248 13556264 0.17362630404186377 2.2457313988357854 chr19 59128983 5836891 0.0987145508658588 0.9752351256094062 chr20 63025520 11101815 0.17614793182190325 0.5639415863123416 chr21 48129895 5480485 0.11386862572627678 0.5090362887346649 chr22 51304566 5135013 0.10008881080876895 0.4180421525279395 chrMT 16571 120791 7.289300585359967 9.915486126585366 chrX 155270560 13971525 0.08998180337599092 0.64052494101946 chrY 59373566 3843452 0.06473338657139105 1.2321468912600708