BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472374.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 = 19,446,924 number of mapped reads = 19,281,553 (99.15%) number of supplementary alignments = 73,404 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,673,870 number of mapped paired reads (second in pair) = 9,607,683 number of mapped paired reads (both in pair) = 19,174,734 number of mapped paired reads (singletons) = 106,819 number of mapped bases = 1,893,354,081 bp number of sequenced bases = 1,893,112,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,982,397 duplication rate = 48.01% >>>>>>> Insert size mean insert size = 20,282.0312 std insert size = 1,402,785.5898 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 54.8639 >>>>>>> ACTG content number of A's = 521,713,508 bp (27.56%) number of C's = 425,812,392 bp (22.49%) number of T's = 522,561,000 bp (27.6%) number of G's = 422,789,108 bp (22.33%) number of N's = 236,144 bp (0.01%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 10,646,120 number of insertions = 114,843 mapped reads with insertion percentage = 0.59% number of deletions = 100,753 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.6116X std coverageData = 17.1386X There is a 5.08% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.28% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 180211226 0.7230121444712468 20.453416569893108 chr2 243199373 158471370 0.6516109315791698 19.904369924692908 chr3 198022430 143471162 0.7245197526361029 16.81069432118441 chr4 191154276 59556496 0.31156245754083994 12.137253842875184 chr5 180915260 61576368 0.3403602769606058 9.771688619328527 chr6 171115067 133879198 0.7823928093953293 15.351351103667932 chr7 159138663 150530713 0.9459091220340339 26.258540300569894 chr8 146364022 98455290 0.6726741220598598 17.221687472620296 chr9 141213431 65700091 0.4652538397710909 12.284508072420726 chr10 135534747 55377532 0.4085854972673539 11.952454765096837 chr11 135006516 55481144 0.4109516017730581 12.520119530103328 chr12 133851895 100499022 0.7508225565278699 17.58906892659997 chr13 115169878 63161898 0.5484237640678928 17.0463563183135 chr14 107349540 30373530 0.28294047650320625 7.591573197223089 chr15 102531392 30680890 0.29923411163675606 8.784634401819769 chr16 90354753 84997839 0.9407124271591999 22.72278853661925 chr17 81195210 98190249 1.2093108571306115 26.90478382665556 chr18 78077248 20948627 0.26830642135337557 8.390985141916499 chr19 59128983 50057739 0.8465854892176988 15.963903545704104 chr20 63025520 61419808 0.9745228282130795 22.374089244627367 chr21 48129895 18587098 0.3861861323404092 23.2335501818236 chr22 51304566 10944064 0.21331559456131058 5.576571029618909 chrMT 16571 35669 2.152495323154909 2.1172393746593503 chrX 155270560 160421064 1.0331711562063022 22.36441942431547 chrY 59373566 325994 0.005490557868799728 0.34871307783112926