BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068125.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 = 3,910,470 number of mapped reads = 3,714,614 (94.99%) number of supplementary alignments = 26,158 (0.67%) number of secondary alignments = 0 number of mapped bases = 248,010,595 bp number of sequenced bases = 247,899,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 284,903 duplication rate = 5.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9859 >>>>>>> ACTG content number of A's = 68,072,657 bp (27.46%) number of C's = 46,248,911 bp (18.66%) number of T's = 77,990,553 bp (31.46%) number of G's = 55,559,190 bp (22.41%) number of N's = 28,185 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,587,007 number of insertions = 17,793 mapped reads with insertion percentage = 0.47% number of deletions = 62,190 mapped reads with deletion percentage = 1.66% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.0801X std coverageData = 1.2349X There is a 6.46% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 21789751 0.0874210499961001 3.0087431087382472 chr2 243199373 26010839 0.1069527387309506 1.132111768960756 chr3 198022430 13419052 0.06776531325264516 0.31078735414416425 chr4 191154276 14273828 0.07467176930951835 0.3607319765149352 chr5 180915260 11422398 0.063136730422851 0.31367618863039853 chr6 171115067 14873339 0.08692010154780817 0.502454472360417 chr7 159138663 19507118 0.1225793759496396 2.377754294455675 chr8 146364022 11086891 0.07574874513902057 1.4271391316350883 chr9 141213431 8403302 0.05950780984848389 0.9165764110805728 chr10 135534747 11612827 0.08568154851095122 0.7420846050639869 chr11 135006516 11736263 0.08693108560774948 0.5359116472344357 chr12 133851895 15547417 0.11615388037651615 0.46282484138172564 chr13 115169878 6429328 0.05582473570042334 0.28256406386473365 chr14 107349540 5231270 0.04873118226682667 0.43221788363702734 chr15 102531392 6319986 0.06163952206949458 0.3203249488183849 chr16 90354753 7077290 0.07832781082363205 0.44530986699427266 chr17 81195210 5644846 0.06952190898945886 0.3507642669822657 chr18 78077248 7815177 0.10009544649934383 1.7532374899379017 chr19 59128983 5289996 0.08946536421910047 1.8846424774988395 chr20 63025520 3850893 0.061100535148301834 0.36867752536715354 chr21 48129895 5385984 0.11190516829508977 0.44253554410513446 chr22 51304566 1892464 0.03688685330658484 0.21942766241638625 chrMT 16571 175124 10.568100899161186 5.995473820435885 chrX 155270560 12483812 0.08040037982731563 0.47260733618361483 chrY 59373566 731400 0.012318613303435404 0.46505934200627236