BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472799.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 95,480,976 number of mapped reads = 95,099,765 (99.6%) number of supplementary alignments = 70,453 (0.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 47,684,160 number of mapped paired reads (second in pair) = 47,415,605 number of mapped paired reads (both in pair) = 94,803,300 number of mapped paired reads (singletons) = 296,465 number of mapped bases = 9,405,184,527 bp number of sequenced bases = 9,404,116,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,604,050 duplication rate = 45.07% >>>>>>> Insert size mean insert size = 13,405.1961 std insert size = 1,146,767.7658 median insert size = 229 >>>>>>> Mapping quality mean mapping quality = 53.6662 >>>>>>> ACTG content number of A's = 2,667,743,345 bp (28.37%) number of C's = 2,032,955,741 bp (21.62%) number of T's = 2,699,651,227 bp (28.71%) number of G's = 2,002,797,295 bp (21.3%) number of N's = 969,309 bp (0.01%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 38,340,989 number of insertions = 388,916 mapped reads with insertion percentage = 0.4% number of deletions = 463,083 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 3.0382X std coverageData = 23.165X There is a 16.01% of reference with a coverageData >= 1X There is a 8.86% of reference with a coverageData >= 2X There is a 5.74% of reference with a coverageData >= 3X There is a 5.01% of reference with a coverageData >= 4X There is a 4.48% of reference with a coverageData >= 5X There is a 4.24% of reference with a coverageData >= 6X There is a 4.04% of reference with a coverageData >= 7X There is a 3.89% of reference with a coverageData >= 8X There is a 3.76% of reference with a coverageData >= 9X There is a 3.64% of reference with a coverageData >= 10X There is a 3.54% of reference with a coverageData >= 11X There is a 3.44% of reference with a coverageData >= 12X There is a 3.35% of reference with a coverageData >= 13X There is a 3.27% of reference with a coverageData >= 14X There is a 3.19% of reference with a coverageData >= 15X There is a 3.11% of reference with a coverageData >= 16X There is a 3.04% of reference with a coverageData >= 17X There is a 2.98% of reference with a coverageData >= 18X There is a 2.91% of reference with a coverageData >= 19X There is a 2.85% of reference with a coverageData >= 20X There is a 2.79% of reference with a coverageData >= 21X There is a 2.74% of reference with a coverageData >= 22X There is a 2.69% of reference with a coverageData >= 23X There is a 2.63% of reference with a coverageData >= 24X There is a 2.58% of reference with a coverageData >= 25X There is a 2.54% of reference with a coverageData >= 26X There is a 2.49% of reference with a coverageData >= 27X There is a 2.45% of reference with a coverageData >= 28X There is a 2.4% of reference with a coverageData >= 29X There is a 2.36% of reference with a coverageData >= 30X There is a 2.32% of reference with a coverageData >= 31X There is a 2.28% of reference with a coverageData >= 32X There is a 2.24% of reference with a coverageData >= 33X There is a 2.21% of reference with a coverageData >= 34X There is a 2.17% of reference with a coverageData >= 35X There is a 2.13% of reference with a coverageData >= 36X There is a 2.1% of reference with a coverageData >= 37X There is a 2.07% of reference with a coverageData >= 38X There is a 2.03% of reference with a coverageData >= 39X There is a 2% of reference with a coverageData >= 40X There is a 1.97% of reference with a coverageData >= 41X There is a 1.94% of reference with a coverageData >= 42X There is a 1.91% of reference with a coverageData >= 43X There is a 1.89% of reference with a coverageData >= 44X There is a 1.86% of reference with a coverageData >= 45X There is a 1.83% of reference with a coverageData >= 46X There is a 1.8% of reference with a coverageData >= 47X There is a 1.78% of reference with a coverageData >= 48X There is a 1.75% of reference with a coverageData >= 49X There is a 1.73% of reference with a coverageData >= 50X There is a 1.71% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 973768443 3.9067844208099287 28.28321372072311 chr2 243199373 885749103 3.642069846125796 26.798419331651637 chr3 198022430 599757670 3.0287360376296766 21.27912080599076 chr4 191154276 494276725 2.585747676395165 20.854179798023406 chr5 180915260 497391760 2.749307935660043 20.61602685310257 chr6 171115067 508007297 2.9688051783306726 21.546619762581226 chr7 159138663 503042228 3.1610308803461544 22.677100971047814 chr8 146364022 359474206 2.45602847672497 19.462406825094206 chr9 141213431 398898857 2.824794031100342 21.540160752228527 chr10 135534747 438814084 3.2376500765519562 23.782322276593604 chr11 135006516 462596028 3.4264718600693316 21.503485786239697 chr12 133851895 502899194 3.757131671538905 23.34102677876594 chr13 115169878 232840241 2.021711275929284 18.111938986850525 chr14 107349540 307412898 2.8636629276660153 21.505427351145034 chr15 102531392 346062726 3.3751880204649907 22.40407556277177 chr16 90354753 296743961 3.28420975264024 21.881451669056812 chr17 81195210 385364873 4.746152796451909 23.593432809883662 chr18 78077248 183068264 2.344706924096505 19.23159729604028 chr19 59128983 283623072 4.7966844280071586 22.5889714551597 chr20 63025520 183531170 2.912013577991899 19.135767153604686 chr21 48129895 107121849 2.2256821669775095 20.74637736408073 chr22 51304566 127954124 2.4940104551318103 17.604341092344345 chrMT 16571 16405835 990.0328887816064 2874.166114929769 chrX 155270560 254114471 1.6365914504333596 13.363454830618654 chrY 59373566 56265448 0.9476514851743956 15.725163876806993