BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819011.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 = 1,574,273 number of mapped reads = 1,545,759 (98.19%) number of supplementary alignments = 22,137 (1.41%) number of secondary alignments = 0 number of mapped bases = 143,153,654 bp number of sequenced bases = 143,063,802 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 585,720 duplication rate = 31.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2523 >>>>>>> ACTG content number of A's = 40,129,235 bp (28.05%) number of C's = 29,496,301 bp (20.62%) number of T's = 41,616,549 bp (29.09%) number of G's = 31,814,862 bp (22.24%) number of N's = 6,855 bp (0%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 918,681 number of insertions = 23,890 mapped reads with insertion percentage = 1.5% number of deletions = 47,373 mapped reads with deletion percentage = 3% homopolymer indels = 39.64% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.587X There is a 2.48% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 14423198 0.057866247001246186 0.9998109001858284 chr2 243199373 11506512 0.047313082505356624 0.874308742949289 chr3 198022430 7704350 0.038906451153033525 0.331393619077002 chr4 191154276 7982039 0.04175705177528961 0.4036631121167853 chr5 180915260 7665488 0.04237059936237551 0.3597125227626077 chr6 171115067 5993208 0.035024431834515195 0.3704700427310439 chr7 159138663 7126745 0.04478324038703278 0.732942661019067 chr8 146364022 13118073 0.08962634956833859 0.5433681461135195 chr9 141213431 6135725 0.043450010077299234 0.5518736179166672 chr10 135534747 7511347 0.05542008353031418 0.7459247606809322 chr11 135006516 4808394 0.03561601426704471 0.37671520515286433 chr12 133851895 6629396 0.04952784568346978 0.38000676126752386 chr13 115169878 3139836 0.027262649353505437 0.27853741081320266 chr14 107349540 3331723 0.031036211240402147 0.3194516906379957 chr15 102531392 3752344 0.036597025816249525 0.322368548319763 chr16 90354753 4613811 0.0510632904945244 0.7126651790495963 chr17 81195210 4890044 0.06022576947581021 0.4729504596973227 chr18 78077248 3299918 0.042264783717786775 0.5517139527025371 chr19 59128983 3066656 0.05186383807751268 0.8581903106234073 chr20 63025520 4299488 0.06821820748166775 0.4787266791300109 chr21 48129895 1940698 0.040322090875120335 0.3610697973473838 chr22 51304566 1108584 0.02160790133182298 0.2683252870335527 chrMT 16571 21675 1.3080079657232515 1.7752209823268545 chrX 155270560 8522583 0.05488859575182829 0.44693578588592464 chrY 59373566 561819 0.009462443269787771 0.6890319034790162