BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975292.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 = 5,569,896 number of mapped reads = 5,523,525 (99.17%) number of supplementary alignments = 30,625 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,760,927 number of mapped paired reads (second in pair) = 2,762,598 number of mapped paired reads (both in pair) = 5,505,558 number of mapped paired reads (singletons) = 17,967 number of mapped bases = 512,221,412 bp number of sequenced bases = 511,924,734 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 297,624 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 85,121.4893 std insert size = 2,798,393.7603 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.9436 >>>>>>> ACTG content number of A's = 149,399,045 bp (29.18%) number of C's = 103,157,767 bp (20.15%) number of T's = 151,400,732 bp (29.57%) number of G's = 107,953,477 bp (21.09%) number of N's = 13,713 bp (0%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 4,320,170 number of insertions = 85,430 mapped reads with insertion percentage = 1.52% number of deletions = 175,437 mapped reads with deletion percentage = 3.11% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.1655X std coverageData = 1.7481X There is a 10.83% of reference with a coverageData >= 1X There is a 3.45% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 46222378 0.18544538751620604 1.656179367579388 chr2 243199373 42465896 0.1746135093859802 1.6645579590413218 chr3 198022430 35603225 0.17979390011525462 0.629297754099231 chr4 191154276 33522787 0.17537032234633348 1.1837009101410088 chr5 180915260 31338703 0.17322310456287657 0.5483223437042462 chr6 171115067 40675167 0.2377065194381743 1.3692157265951153 chr7 159138663 28976968 0.18208628534223642 1.6490525516093266 chr8 146364022 25701477 0.17559969074913778 0.7352671138661365 chr9 141213431 21472196 0.15205491324688514 2.177117661352088 chr10 135534747 28184554 0.20795076261882867 5.519911385342957 chr11 135006516 18345593 0.13588672268233334 1.4546846466317864 chr12 133851895 22345122 0.1669391531587954 0.5428756374711652 chr13 115169878 17339583 0.15055658042808728 0.5145059937054579 chr14 107349540 14796644 0.13783611927913245 0.5437462682195117 chr15 102531392 14331223 0.1397740020929395 0.49508519806691037 chr16 90354753 16798041 0.18591209031361083 2.8028215298324564 chr17 81195210 10060674 0.1239072354145029 1.198848090073261 chr18 78077248 14153805 0.18127950667523526 2.1163782063378087 chr19 59128983 6180955 0.10453342314377367 1.0217981242598537 chr20 63025520 10573953 0.16777256260638548 0.6056117482542356 chr21 48129895 6275183 0.1303801514630356 0.6844710533999258 chr22 51304566 4744921 0.09248535500719371 0.4102621821391341 chrMT 16571 102470 6.183694405889807 6.971863460281334 chrX 155270560 15558003 0.10019931015898957 0.6810379167413109 chrY 59373566 6451891 0.1086660518251506 2.204516218594727