BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008832.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,533,904 number of mapped reads = 1,386,527 (90.39%) number of supplementary alignments = 8,175 (0.53%) number of secondary alignments = 0 number of mapped bases = 90,610,827 bp number of sequenced bases = 90,564,664 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,274 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1149 >>>>>>> ACTG content number of A's = 24,833,385 bp (27.42%) number of C's = 16,697,665 bp (18.44%) number of T's = 28,647,417 bp (31.63%) number of G's = 20,269,188 bp (22.38%) number of N's = 117,009 bp (0.13%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 730,652 number of insertions = 6,360 mapped reads with insertion percentage = 0.45% number of deletions = 25,905 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.2976X There is a 2.51% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% 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% 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 7424936 0.02978903711537794 0.5384521037859794 chr2 243199373 9589116 0.03942903257402724 0.33343991587932803 chr3 198022430 6799570 0.034337372791557 0.2206275871956103 chr4 191154276 5295518 0.027702848771219746 0.1999143714400532 chr5 180915260 4001852 0.02212003564541764 0.1668531442513081 chr6 171115067 5236701 0.03060338923865775 0.21685376601978276 chr7 159138663 4775129 0.030006089720635645 0.37595744153813154 chr8 146364022 7421897 0.05070847943765853 0.39820600913598236 chr9 141213431 2632833 0.018644352604108884 0.21829960472867577 chr10 135534747 5603324 0.041342343008173396 0.45741786971546966 chr11 135006516 4372724 0.032388984839813215 0.26316541885635325 chr12 133851895 3399816 0.025399834645598404 0.17994586317649297 chr13 115169878 2633597 0.02286706425094937 0.16842655113794144 chr14 107349540 2848416 0.02653403079323861 0.18864086164283192 chr15 102531392 1901150 0.018542126103193838 0.1531976636204801 chr16 90354753 2228041 0.024658813466071895 0.2342763360943307 chr17 81195210 2699072 0.0332417638922296 0.2438680092813677 chr18 78077248 1944335 0.02490270917335611 0.37934433400965156 chr19 59128983 1783133 0.030156666147970107 0.3398537744126133 chr20 63025520 2039344 0.03235743235438597 0.20519516021222448 chr21 48129895 750774 0.015598912069099673 0.15415661096861638 chr22 51304566 1014169 0.019767616784829637 0.15579166151685792 chrMT 16571 20558 1.2406010500271558 1.5113854719600854 chrX 155270560 3942543 0.025391439304398723 0.19531005044343694 chrY 59373566 252279 0.004249012094035248 0.1571903772385238