BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818769.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 285,828 number of mapped reads = 265,574 (92.91%) number of supplementary alignments = 2,263 (0.79%) number of secondary alignments = 0 number of mapped bases = 18,007,078 bp number of sequenced bases = 17,999,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,682 duplication rate = 11.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0032 >>>>>>> ACTG content number of A's = 5,273,274 bp (29.3%) number of C's = 3,666,814 bp (20.37%) number of T's = 5,118,447 bp (28.44%) number of G's = 3,939,648 bp (21.89%) number of N's = 1,248 bp (0.01%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 94,267 number of insertions = 2,189 mapped reads with insertion percentage = 0.81% number of deletions = 4,675 mapped reads with deletion percentage = 1.74% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0058X std coverageData = 0.1061X There is a 0.48% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 1469089 0.0058940234295344045 0.1396239007021142 chr2 243199373 1616672 0.006647517138130121 0.15294990487338403 chr3 198022430 1226373 0.006193101458253997 0.0923637872001524 chr4 191154276 1217294 0.00636812330580562 0.09790123089715064 chr5 180915260 1114272 0.006159082434505525 0.09234125057226511 chr6 171115067 1050706 0.006140347652728909 0.0950258204532679 chr7 159138663 997107 0.006265648970545894 0.10345977635306153 chr8 146364022 927113 0.006334295732868013 0.09885671485129302 chr9 141213431 767908 0.005437924668794429 0.0917381409589971 chr10 135534747 891636 0.006578652483853458 0.112368612001219 chr11 135006516 847058 0.006274200868941763 0.09657800736279903 chr12 133851895 803660 0.006004098783958195 0.09416751002240453 chr13 115169878 578622 0.005024074089928271 0.08268011437743666 chr14 107349540 566026 0.005272738010800978 0.09060562000861479 chr15 102531392 524112 0.005111722271360561 0.08430664548105118 chr16 90354753 517299 0.005725199647217231 0.10951093309457567 chr17 81195210 458654 0.00564878149831745 0.08898759955965058 chr18 78077248 499249 0.006394295557138489 0.11497261656043743 chr19 59128983 339215 0.005736865117399364 0.12141205772543753 chr20 63025520 376809 0.005978673400869996 0.09352010715777799 chr21 48129895 248796 0.005169261225273814 0.08780267436805204 chr22 51304566 206882 0.004032428614638315 0.07864187654123449 chrMT 16571 11264 0.6797417174582101 1.067437890193485 chrX 155270560 556175 0.003581973298737378 0.072262645955087 chrY 59373566 195087 0.003285755145648486 0.13587659006985697