BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094005.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 423,230 number of mapped reads = 211,030 (49.86%) number of supplementary alignments = 1,117 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 105,144 number of mapped paired reads (second in pair) = 105,886 number of mapped paired reads (both in pair) = 207,470 number of mapped paired reads (singletons) = 3,560 number of mapped bases = 28,228,054 bp number of sequenced bases = 27,692,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 206,927 duplication rate = 42.84% >>>>>>> Insert size mean insert size = 76,809.329 std insert size = 2,866,121.6797 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 18.5983 >>>>>>> ACTG content number of A's = 7,652,674 bp (27.63%) number of C's = 5,959,632 bp (21.52%) number of T's = 7,546,710 bp (27.25%) number of G's = 6,533,471 bp (23.59%) number of N's = 338 bp (0%) GC percentage = 45.11% >>>>>>> Mismatches and indels general error rate = 0.0392 number of mismatches = 1,098,222 number of insertions = 3,107 mapped reads with insertion percentage = 1.39% number of deletions = 72,989 mapped reads with deletion percentage = 33.39% homopolymer indels = 32.46% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 11.0086X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 1236419 0.004960545313947282 7.670364591926418 chr2 243199373 889425 0.0036571845931527135 3.0097151596567198 chr3 198022430 32081 1.6200689992542763E-4 0.10900534257669765 chr4 191154276 7006 3.6651024222968465E-5 0.012051012581591415 chr5 180915260 157766 8.720436297081849E-4 0.8021724822136886 chr6 171115067 171797 0.0010039852305933994 0.5262353775896917 chr7 159138663 167685 0.001053703712466153 1.0086127709513193 chr8 146364022 2011085 0.013740296095443456 10.803019823701451 chr9 141213431 991296 0.007019842184841469 4.1651069136475884 chr10 135534747 61490 4.536843972564467E-4 0.2766317585287534 chr11 135006516 258556 0.001915137192341146 1.5823103083303982 chr12 133851895 123181 9.202783419689351E-4 0.6940642258987647 chr13 115169878 7058 6.12833852268212E-5 0.030556569743411477 chr14 107349540 17459 1.6263693351643613E-4 0.09213283312471063 chr15 102531392 6704 6.538485306041686E-5 0.018460998219045694 chr16 90354753 63761 7.056740003483823E-4 0.31742376596910965 chr17 81195210 194572 0.0023963482574895735 1.5989599286478937 chr18 78077248 39338 5.03834356456826E-4 0.32250516860909184 chr19 59128983 8651 1.463072686367699E-4 0.038485457262435054 chr20 63025520 48228 7.652138371884912E-4 0.38403613345799376 chr21 48129895 971 2.0174571334510494E-5 0.00485180953131669 chr22 51304566 29930 5.833788750888177E-4 0.23813702125533887 chrMT 16571 13207352 797.0159917928912 4043.602360950964 chrX 155270560 8030642 0.05172031323903256 18.791344977089388 chrY 59373566 465601 0.007841890446667799 5.041841149392893