BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094056.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 = 392,084 number of mapped reads = 377,072 (96.17%) number of supplementary alignments = 12,725 (3.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 189,395 number of mapped paired reads (second in pair) = 187,677 number of mapped paired reads (both in pair) = 374,650 number of mapped paired reads (singletons) = 2,422 number of mapped bases = 50,689,459 bp number of sequenced bases = 49,503,840 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 355,192 duplication rate = 50.38% >>>>>>> Insert size mean insert size = 548,853.1036 std insert size = 6,654,140.843 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 44.8386 >>>>>>> ACTG content number of A's = 13,536,357 bp (27.34%) number of C's = 11,209,032 bp (22.64%) number of T's = 13,134,969 bp (26.53%) number of G's = 11,622,895 bp (23.48%) number of N's = 587 bp (0%) GC percentage = 46.12% >>>>>>> Mismatches and indels general error rate = 0.0428 number of mismatches = 2,049,339 number of insertions = 37,315 mapped reads with insertion percentage = 9.75% number of deletions = 161,883 mapped reads with deletion percentage = 39.9% homopolymer indels = 30.08% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 4.3793X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 582917 0.0023386782253994867 0.8205918996497655 chr2 243199373 1813972 0.007458785677050245 2.3544860117291546 chr3 198022430 938236 0.0047380289192491985 1.5831515991691676 chr4 191154276 1100387 0.00575653876557802 2.529971896671579 chr5 180915260 293947 0.001624777257595628 0.5474098340541296 chr6 171115067 1756041 0.010262340019420967 4.49404912652444 chr7 159138663 995242 0.006253929631167003 2.2483529174769004 chr8 146364022 910013 0.0062174637425582635 1.9101167704079358 chr9 141213431 787251 0.005574901724468404 2.7831478345554586 chr10 135534747 1135345 0.008376781785706952 2.7683419087628174 chr11 135006516 1481332 0.010972300033281356 2.7466862178819107 chr12 133851895 1699248 0.012694986499817578 4.16920997308183 chr13 115169878 1446253 0.012557563011397824 3.9808276291374947 chr14 107349540 161777 0.001507011581046365 0.5220809547720607 chr15 102531392 514486 0.005017838829302151 1.540621520142977 chr16 90354753 438843 0.004856888934221313 1.1917070100045468 chr17 81195210 1309047 0.01612221952501878 4.3283483227423485 chr18 78077248 282860 0.0036228223617717674 0.9990212971579923 chr19 59128983 243661 0.004120838675679573 1.2643840003995637 chr20 63025520 204437 0.0032437177828917555 0.7236298454510774 chr21 48129895 125461 0.0026067166778568703 0.5028486466315262 chr22 51304566 157500 0.0030699021993481047 0.6799290179921877 chrMT 16571 3842958 231.90863556816126 957.8903259554448 chrX 155270560 28211488 0.18169244704211795 12.836326183508087 chrY 59373566 256757 0.004324432862934323 1.514835536401405