BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617677.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 3,759,980 number of mapped reads = 3,713,917 (98.77%) number of supplementary alignments = 60,298 (1.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,856,578 number of mapped paired reads (second in pair) = 1,857,339 number of mapped paired reads (both in pair) = 3,704,386 number of mapped paired reads (singletons) = 9,531 number of mapped bases = 359,451,832 bp number of sequenced bases = 359,318,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 178,182 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 143,604.6632 std insert size = 3,612,288.2992 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 52.9211 >>>>>>> ACTG content number of A's = 103,577,056 bp (28.83%) number of C's = 77,622,287 bp (21.6%) number of T's = 103,458,706 bp (28.79%) number of G's = 74,652,597 bp (20.78%) number of N's = 7,621 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,915,843 number of insertions = 47,875 mapped reads with insertion percentage = 1.25% number of deletions = 55,310 mapped reads with deletion percentage = 1.45% homopolymer indels = 40.27% >>>>>>> Coverage mean coverageData = 0.1161X std coverageData = 1.5971X There is a 8.28% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 33653180 0.1350174369274691 4.044108606173277 chr2 243199373 28182306 0.11588149119118 1.045419327606329 chr3 198022430 23018078 0.11623975122414162 0.4610661751010567 chr4 191154276 22068105 0.11544656735798052 1.1248790926240813 chr5 180915260 20225841 0.11179731881102788 0.4105155205276329 chr6 171115067 27652461 0.1616015555193629 0.7483574394234007 chr7 159138663 21001473 0.1319696458678932 1.2281741772972632 chr8 146364022 17207056 0.11756342689189014 1.5370711013186755 chr9 141213431 15328106 0.10854566659456068 1.6130923982299135 chr10 135534747 19030017 0.14040692458001194 2.914277754792573 chr11 135006516 12717740 0.09420093471636584 0.8486043874863786 chr12 133851895 15669077 0.11706279541279561 0.528837056428198 chr13 115169878 11858679 0.10296684520235404 0.3901711241135952 chr14 107349540 10525935 0.09805291201061504 0.3954497422480499 chr15 102531392 10360283 0.10104498532507976 0.38451570343253166 chr16 90354753 11715847 0.12966497733661006 0.8842193087180988 chr17 81195210 9345972 0.11510496739893893 0.596954008766683 chr18 78077248 9507642 0.12177224791529538 1.7124544566913897 chr19 59128983 8607464 0.1455709799710237 1.9711479614830303 chr20 63025520 7711305 0.12235210435391886 0.4992803816216679 chr21 48129895 4950287 0.10285264491019563 0.8615575940651177 chr22 51304566 5178589 0.10093816990869779 0.9304925870669996 chrMT 16571 461955 27.87731579264981 9.450021460607562 chrX 155270560 8965056 0.057738285995748324 0.4693433224511587 chrY 59373566 4509378 0.07594925324175408 1.5952746912265625