BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818937.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 = 597,333 number of mapped reads = 586,741 (98.23%) number of supplementary alignments = 6,234 (1.04%) number of secondary alignments = 0 number of mapped bases = 54,497,788 bp number of sequenced bases = 54,468,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,344 duplication rate = 18.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2737 >>>>>>> ACTG content number of A's = 15,377,442 bp (28.23%) number of C's = 11,470,929 bp (21.06%) number of T's = 14,958,422 bp (27.46%) number of G's = 12,659,055 bp (23.24%) number of N's = 2,374 bp (0%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 341,704 number of insertions = 6,075 mapped reads with insertion percentage = 1.01% number of deletions = 16,127 mapped reads with deletion percentage = 2.69% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 0.227X There is a 1.26% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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% 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 6471187 0.025962571222641007 0.36159685461105456 chr2 243199373 4707844 0.019357961091453966 0.3004722439583123 chr3 198022430 3608601 0.018223193200891434 0.17870430567991946 chr4 191154276 3368999 0.01762450242023359 0.18091218765867742 chr5 180915260 2820651 0.015591006529797431 0.16786918031750978 chr6 171115067 2880361 0.016832889414700108 0.1767063350500924 chr7 159138663 2743975 0.017242667170076702 0.19872477133104421 chr8 146364022 3548302 0.024242993267840098 0.2233396637244965 chr9 141213431 2019131 0.014298434544799071 0.23927955271236911 chr10 135534747 2743578 0.02024261719395101 0.26443730114277403 chr11 135006516 2328735 0.01724905633443648 0.1921505839875756 chr12 133851895 2411651 0.018017309355239236 0.18236125033359718 chr13 115169878 872449 0.00757532277667256 0.11407735871048881 chr14 107349540 1313365 0.012234472546412401 0.15744293251155897 chr15 102531392 1574519 0.015356457854390585 0.16364927468075205 chr16 90354753 1680103 0.018594517103046035 0.23950827692642263 chr17 81195210 1229436 0.015141730651352462 0.17301655109524502 chr18 78077248 1351732 0.017312751596982517 0.3047263290425544 chr19 59128983 893041 0.015103270083302464 0.3024142361218469 chr20 63025520 1179347 0.01871221371914107 0.18712893106662368 chr21 48129895 714521 0.014845679592693896 0.17576383948237692 chr22 51304566 716678 0.01396908805348826 0.16977001724224766 chrMT 16571 93692 5.653973809667491 4.465070257517358 chrX 155270560 3071504 0.01978162505500077 0.20898407861443577 chrY 59373566 154386 0.002600248063254277 0.14847517248754502